3S6L | pdb_00003s6l

Crystal structure of a YadA-like head domain of the trimeric autotransporter adhesin BoaA from Burkholderia pseudomallei solved by iodide ion SAD phasing

PDB DOI: https://doi.org/10.2210/pdb3S6L/pdb

Classification: CELL ADHESION
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-25 Released: 2011-06-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.207 (Depositor), 0.212 (DCC)
R-Value Work:
0.175 (Depositor), 0.178 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a YadA-like head domain of the trimeric autotransporter adhesin BoaA from Burkholderia pseudomallei

Edwards, T.E., Gardberg, A.S., Lafontaine, E.R., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 89.78 kDa
Atom Count: 5,354
Modeled Residue Count: 777
Deposited Residue Count: 890
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hep_Hag family	A, B, C, D, E	178	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: BURPS1710b_A2381
UniProt
Find proteins for Q3JFX2 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JFX2 Go to UniProtKB: Q3JFX2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3JFX2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AC [auth E] SDF format, chain BA [auth B] SDF format, chain BC [auth E] SDF format, chain CA [auth B] SDF format, chain CC [auth E] SDF format, chain DA [auth B] SDF format, chain DC [auth E] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain FC [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain HC [auth E] SDF format, chain I [auth A] SDF format, chain IB [auth D] SDF format, chain IC [auth E] SDF format, chain J [auth A] SDF format, chain JB [auth D] SDF format, chain JC [auth E] SDF format, chain K [auth A] SDF format, chain KB [auth D] SDF format, chain KC [auth E] SDF format, chain LB [auth D] SDF format, chain LC [auth E] SDF format, chain M [auth A] SDF format, chain MB [auth D] SDF format, chain N [auth A] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZB [auth E] SDF format, chain L [auth A] SDF format, chain GC [auth E] SDF format, chain EC [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain CC [auth E] MOL2 format, chain DA [auth B] MOL2 format, chain DC [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain FC [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain HC [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain IC [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth D] MOL2 format, chain KC [auth E] MOL2 format, chain LB [auth D] MOL2 format, chain LC [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth E] MOL2 format, chain L [auth A] MOL2 format, chain GC [auth E] MOL2 format, chain EC [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain AC [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain BC [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain CC [auth E] mmCIF format, chain DA [auth B] mmCIF format, chain DC [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain FC [auth E] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain HC [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain IC [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain JC [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth D] mmCIF format, chain KC [auth E] mmCIF format, chain LB [auth D] mmCIF format, chain LC [auth E] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZB [auth E] mmCIF format, chain L [auth A] mmCIF format, chain GC [auth E] mmCIF format, chain EC [auth E]	AA [auth B] AC [auth E] BA [auth B] BC [auth E] CA [auth B] AA [auth B], AC [auth E], BA [auth B], BC [auth E], CA [auth B], CC [auth E], DA [auth B], DC [auth E], EA [auth B], EC [auth E], F [auth A], FA [auth B], FC [auth E], G [auth A], GA [auth B], GB [auth D], GC [auth E], H [auth A], HA [auth B], HB [auth D], HC [auth E], I [auth A], IB [auth D], IC [auth E], J [auth A], JB [auth D], JC [auth E], K [auth A], KB [auth D], KC [auth E], L [auth A], LB [auth D], LC [auth E], M [auth A], MB [auth D], N [auth A], NB [auth D], O [auth A], OB [auth D], P [auth A], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZB [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AC [auth E] Focus chain BA [auth B] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain DA [auth B] Focus chain DC [auth E] Focus chain EA [auth B] Focus chain EC [auth E] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FC [auth E] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GC [auth E] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth E] Focus chain I [auth A] Focus chain IB [auth D] Focus chain IC [auth E] Focus chain J [auth A] Focus chain JB [auth D] Focus chain JC [auth E] Focus chain K [auth A] Focus chain KB [auth D] Focus chain KC [auth E] Focus chain L [auth A] Focus chain LB [auth D] Focus chain LC [auth E] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZB [auth E] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth E] Focus chain BA [auth B] Focus chain BC [auth E] Focus chain CA [auth B] Focus chain CC [auth E] Focus chain DA [auth B] Focus chain DC [auth E] Focus chain EA [auth B] Focus chain EC [auth E] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FC [auth E] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GC [auth E] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth E] Focus chain I [auth A] Focus chain IB [auth D] Focus chain IC [auth E] Focus chain J [auth A] Focus chain JB [auth D] Focus chain JC [auth E] Focus chain K [auth A] Focus chain KB [auth D] Focus chain KC [auth E] Focus chain L [auth A] Focus chain LB [auth D] Focus chain LC [auth E] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZB [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain MC [auth E] SDF format, chain NC [auth E] SDF format, chain OC [auth E] SDF format, chain PB [auth D] SDF format, chain PC [auth E] SDF format, chain Q [auth A] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RB [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain MC [auth E] MOL2 format, chain NC [auth E] MOL2 format, chain OC [auth E] MOL2 format, chain PB [auth D] MOL2 format, chain PC [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain MC [auth E] mmCIF format, chain NC [auth E] mmCIF format, chain OC [auth E] mmCIF format, chain PB [auth D] mmCIF format, chain PC [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth D] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain ZA [auth C]	AB [auth C] BB [auth C] IA [auth B] JA [auth B] KA [auth B] AB [auth C], BB [auth C], IA [auth B], JA [auth B], KA [auth B], MC [auth E], NC [auth E], OC [auth E], PB [auth D], PC [auth E], Q [auth A], QB [auth D], R [auth A], RB [auth D], S [auth A], T [auth A], ZA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MC [auth E] Focus chain NC [auth E] Focus chain OC [auth E] Focus chain PB [auth D] Focus chain PC [auth E] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MC [auth E] Focus chain NC [auth E] Focus chain OC [auth E] Focus chain PB [auth D] Focus chain PC [auth E] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RB [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain ZA [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain QC [auth E] SDF format, chain RC [auth E] SDF format, chain SB [auth D] SDF format, chain SC [auth E] SDF format, chain TB [auth D] SDF format, chain TC [auth E] SDF format, chain UB [auth D] SDF format, chain UC [auth E] SDF format, chain V [auth A] SDF format, chain VB [auth D] SDF format, chain VC [auth E] SDF format, chain W [auth A] SDF format, chain WB [auth D] SDF format, chain X [auth A] SDF format, chain XB [auth D] SDF format, chain YB [auth D] SDF format, chain U [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain QC [auth E] MOL2 format, chain RC [auth E] MOL2 format, chain SB [auth D] MOL2 format, chain SC [auth E] MOL2 format, chain TB [auth D] MOL2 format, chain TC [auth E] MOL2 format, chain UB [auth D] MOL2 format, chain UC [auth E] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth D] MOL2 format, chain VC [auth E] MOL2 format, chain W [auth A] MOL2 format, chain WB [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth D] MOL2 format, chain YB [auth D] MOL2 format, chain U [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain QC [auth E] mmCIF format, chain RC [auth E] mmCIF format, chain SB [auth D] mmCIF format, chain SC [auth E] mmCIF format, chain TB [auth D] mmCIF format, chain TC [auth E] mmCIF format, chain UB [auth D] mmCIF format, chain UC [auth E] mmCIF format, chain V [auth A] mmCIF format, chain VB [auth D] mmCIF format, chain VC [auth E] mmCIF format, chain W [auth A] mmCIF format, chain WB [auth D] mmCIF format, chain X [auth A] mmCIF format, chain XB [auth D] mmCIF format, chain YB [auth D] mmCIF format, chain U [auth A]	CB [auth C] DB [auth C] EB [auth C] FB [auth C] LA [auth B] CB [auth C], DB [auth C], EB [auth C], FB [auth C], LA [auth B], MA [auth B], NA [auth B], OA [auth B], QC [auth E], RC [auth E], SB [auth D], SC [auth E], TB [auth D], TC [auth E], U [auth A], UB [auth D], UC [auth E], V [auth A], VB [auth D], VC [auth E], W [auth A], WB [auth D], X [auth A], XB [auth D], YB [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain QC [auth E] Focus chain RC [auth E] Focus chain SB [auth D] Focus chain SC [auth E] Focus chain TB [auth D] Focus chain TC [auth E] Focus chain U [auth A] Focus chain UB [auth D] Focus chain UC [auth E] Focus chain V [auth A] Focus chain VB [auth D] Focus chain VC [auth E] Focus chain W [auth A] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XB [auth D] Focus chain YB [auth D] Interactions & Density Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain QC [auth E] Focus chain RC [auth E] Focus chain SB [auth D] Focus chain SC [auth E] Focus chain TB [auth D] Focus chain TC [auth E] Focus chain U [auth A] Focus chain UB [auth D] Focus chain UC [auth E] Focus chain V [auth A] Focus chain VB [auth D] Focus chain VC [auth E] Focus chain W [auth A] Focus chain WB [auth D] Focus chain X [auth A] Focus chain XB [auth D] Focus chain YB [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.207 (Depositor), 0.212 (DCC)
R-Value Work: 0.175 (Depositor), 0.178 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data:

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144	α = 90
b = 144	β = 90
c = 144	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-09-20
Changes: Data collection
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description