4LW9 | pdb_00004lw9

Crystal structure of Vibrio cholera major pseudopilin EpsG

PDB DOI: https://doi.org/10.2210/pdb4LW9/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-26 Released: 2014-07-16
Deposition Author(s): Vago, F.S., Raghunathan, K., Jens, J.C., Wedemeyer, W.J., Bagdasarian, M., Brunzelle, J.S., Arvidson, D.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.245 (Depositor), 0.250 (DCC)
R-Value Work:
0.202 (Depositor), 0.209 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Vibrio cholera major pseudopilin EpsG

Vago, F.S., Raghunathan, K., Jens, J.C., Wedemeyer, W.J., Bagdasarian, M., Brunzelle, J.S., Arvidson, D.N.

To be published.

Macromolecule Content

Total Structure Weight: 167.5 kDa
Atom Count: 11,720
Modeled Residue Count: 1,414
Deposited Residue Count: 1,440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II secretion system protein G	A B C D E A, B, C, D, E, F, G [auth I], H [auth J], I [auth K], J [auth L], K [auth Q], L [auth R]	120	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: epsG, VC_2730
UniProt
Find proteins for P45773 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P45773 Go to UniProtKB: P45773
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45773
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain ZB [auth K] SDF format, chain XA [auth E] SDF format, chain T [auth A] SDF format, chain SC [auth R] SDF format, chain RB [auth J] SDF format, chain OA [auth D] SDF format, chain NC [auth Q] SDF format, chain LB [auth I] SDF format, chain HA [auth C] SDF format, chain GC [auth L] SDF format, chain EB [auth F] SDF format, chain AA [auth B] MOL2 format, chain ZB [auth K] MOL2 format, chain XA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain SC [auth R] MOL2 format, chain RB [auth J] MOL2 format, chain OA [auth D] MOL2 format, chain NC [auth Q] MOL2 format, chain LB [auth I] MOL2 format, chain HA [auth C] MOL2 format, chain GC [auth L] MOL2 format, chain EB [auth F] MOL2 format, chain AA [auth B] mmCIF format, chain ZB [auth K] mmCIF format, chain XA [auth E] mmCIF format, chain T [auth A] mmCIF format, chain SC [auth R] mmCIF format, chain RB [auth J] mmCIF format, chain OA [auth D] mmCIF format, chain NC [auth Q] mmCIF format, chain LB [auth I] mmCIF format, chain HA [auth C] mmCIF format, chain GC [auth L] mmCIF format, chain EB [auth F] mmCIF format, chain AA [auth B]	AA [auth B] EB [auth F] GC [auth L] HA [auth C] LB [auth I] AA [auth B], EB [auth F], GC [auth L], HA [auth C], LB [auth I], NC [auth Q], OA [auth D], RB [auth J], SC [auth R], T [auth A], XA [auth E], ZB [auth K]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain EB [auth F] Focus chain GC [auth L] Focus chain HA [auth C] Focus chain LB [auth I] Focus chain NC [auth Q] Focus chain OA [auth D] Focus chain RB [auth J] Focus chain SC [auth R] Focus chain T [auth A] Focus chain XA [auth E] Focus chain ZB [auth K] Interactions & Density Focus chain AA [auth B] Focus chain EB [auth F] Focus chain GC [auth L] Focus chain HA [auth C] Focus chain LB [auth I] Focus chain NC [auth Q] Focus chain OA [auth D] Focus chain RB [auth J] Focus chain SC [auth R] Focus chain T [auth A] Focus chain XA [auth E] Focus chain ZB [auth K]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain UC [auth R] SDF format, chain U [auth A] SDF format, chain SB [auth J] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain OC [auth Q] SDF format, chain NB [auth I] SDF format, chain MB [auth I] SDF format, chain IA [auth C] SDF format, chain GB [auth F] SDF format, chain CA [auth B] SDF format, chain BC [auth K] SDF format, chain AC [auth K] SDF format, chain AB [auth E] MOL2 format, chain UC [auth R] MOL2 format, chain U [auth A] MOL2 format, chain SB [auth J] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain OC [auth Q] MOL2 format, chain NB [auth I] MOL2 format, chain MB [auth I] MOL2 format, chain IA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain CA [auth B] MOL2 format, chain BC [auth K] MOL2 format, chain AC [auth K] MOL2 format, chain AB [auth E] mmCIF format, chain UC [auth R] mmCIF format, chain U [auth A] mmCIF format, chain SB [auth J] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain OC [auth Q] mmCIF format, chain NB [auth I] mmCIF format, chain MB [auth I] mmCIF format, chain IA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain CA [auth B] mmCIF format, chain BC [auth K] mmCIF format, chain AC [auth K] mmCIF format, chain AB [auth E]	AB [auth E] AC [auth K] BC [auth K] CA [auth B] GB [auth F] AB [auth E], AC [auth K], BC [auth K], CA [auth B], GB [auth F], IA [auth C], MB [auth I], NB [auth I], OC [auth Q], QA [auth D], RA [auth D], SB [auth J], U [auth A], UC [auth R]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth E] Focus chain AC [auth K] Focus chain BC [auth K] Focus chain CA [auth B] Focus chain GB [auth F] Focus chain IA [auth C] Focus chain MB [auth I] Focus chain NB [auth I] Focus chain OC [auth Q] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SB [auth J] Focus chain U [auth A] Focus chain UC [auth R] Interactions & Density Focus chain AB [auth E] Focus chain AC [auth K] Focus chain BC [auth K] Focus chain CA [auth B] Focus chain GB [auth F] Focus chain IA [auth C] Focus chain MB [auth I] Focus chain NB [auth I] Focus chain OC [auth Q] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SB [auth J] Focus chain U [auth A] Focus chain UC [auth R]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain WB [auth K] SDF format, chain VB [auth K] SDF format, chain VA [auth E] SDF format, chain UB [auth K] SDF format, chain UA [auth E] SDF format, chain TB [auth K] SDF format, chain TA [auth E] SDF format, chain SA [auth E] SDF format, chain PC [auth R] SDF format, chain PB [auth J] SDF format, chain OB [auth J] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth D] SDF format, chain KC [auth Q] SDF format, chain KA [auth D] SDF format, chain JC [auth Q] SDF format, chain JB [auth I] SDF format, chain JA [auth D] SDF format, chain IC [auth Q] SDF format, chain IB [auth I] SDF format, chain HB [auth I] SDF format, chain FC [auth L] SDF format, chain FB [auth F] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DC [auth L] SDF format, chain DA [auth C] SDF format, chain CC [auth L] SDF format, chain BB [auth F] MOL2 format, chain X [auth B] MOL2 format, chain WB [auth K] MOL2 format, chain VB [auth K] MOL2 format, chain VA [auth E] MOL2 format, chain UB [auth K] MOL2 format, chain UA [auth E] MOL2 format, chain TB [auth K] MOL2 format, chain TA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain PC [auth R] MOL2 format, chain PB [auth J] MOL2 format, chain OB [auth J] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain KC [auth Q] MOL2 format, chain KA [auth D] MOL2 format, chain JC [auth Q] MOL2 format, chain JB [auth I] MOL2 format, chain JA [auth D] MOL2 format, chain IC [auth Q] MOL2 format, chain IB [auth I] MOL2 format, chain HB [auth I] MOL2 format, chain FC [auth L] MOL2 format, chain FB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DC [auth L] MOL2 format, chain DA [auth C] MOL2 format, chain CC [auth L] MOL2 format, chain BB [auth F] mmCIF format, chain X [auth B] mmCIF format, chain WB [auth K] mmCIF format, chain VB [auth K] mmCIF format, chain VA [auth E] mmCIF format, chain UB [auth K] mmCIF format, chain UA [auth E] mmCIF format, chain TB [auth K] mmCIF format, chain TA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain PC [auth R] mmCIF format, chain PB [auth J] mmCIF format, chain OB [auth J] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain KC [auth Q] mmCIF format, chain KA [auth D] mmCIF format, chain JC [auth Q] mmCIF format, chain JB [auth I] mmCIF format, chain JA [auth D] mmCIF format, chain IC [auth Q] mmCIF format, chain IB [auth I] mmCIF format, chain HB [auth I] mmCIF format, chain FC [auth L] mmCIF format, chain FB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DC [auth L] mmCIF format, chain DA [auth C] mmCIF format, chain CC [auth L] mmCIF format, chain BB [auth F]	BB [auth F] CC [auth L] DA [auth C] DC [auth L] EA [auth C] BB [auth F], CC [auth L], DA [auth C], DC [auth L], EA [auth C], FA [auth C], FB [auth F], FC [auth L], HB [auth I], IB [auth I], IC [auth Q], JA [auth D], JB [auth I], JC [auth Q], KA [auth D], KC [auth Q], LA [auth D], M [auth A], N [auth A], O [auth A], OB [auth J], PB [auth J], PC [auth R], SA [auth E], TA [auth E], TB [auth K], UA [auth E], UB [auth K], VA [auth E], VB [auth K], WB [auth K], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain CC [auth L] Focus chain DA [auth C] Focus chain DC [auth L] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain FC [auth L] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain IC [auth Q] Focus chain JA [auth D] Focus chain JB [auth I] Focus chain JC [auth Q] Focus chain KA [auth D] Focus chain KC [auth Q] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth J] Focus chain PB [auth J] Focus chain PC [auth R] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain TB [auth K] Focus chain UA [auth E] Focus chain UB [auth K] Focus chain VA [auth E] Focus chain VB [auth K] Focus chain WB [auth K] Focus chain X [auth B] Interactions & Density Focus chain BB [auth F] Focus chain CC [auth L] Focus chain DA [auth C] Focus chain DC [auth L] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain FC [auth L] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain IC [auth Q] Focus chain JA [auth D] Focus chain JB [auth I] Focus chain JC [auth Q] Focus chain KA [auth D] Focus chain KC [auth Q] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OB [auth J] Focus chain PB [auth J] Focus chain PC [auth R] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain TB [auth K] Focus chain UA [auth E] Focus chain UB [auth K] Focus chain VA [auth E] Focus chain VB [auth K] Focus chain WB [auth K] Focus chain X [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain YB [auth K] SDF format, chain WA [auth E] SDF format, chain W [auth B] SDF format, chain QC [auth R] SDF format, chain QB [auth J] SDF format, chain Q [auth A] SDF format, chain NA [auth D] SDF format, chain MC [auth Q] SDF format, chain LC [auth Q] SDF format, chain KB [auth I] SDF format, chain GA [auth C] SDF format, chain EC [auth L] SDF format, chain DB [auth F] SDF format, chain CB [auth F] MOL2 format, chain YB [auth K] MOL2 format, chain WA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain QC [auth R] MOL2 format, chain QB [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain MC [auth Q] MOL2 format, chain LC [auth Q] MOL2 format, chain KB [auth I] MOL2 format, chain GA [auth C] MOL2 format, chain EC [auth L] MOL2 format, chain DB [auth F] MOL2 format, chain CB [auth F] mmCIF format, chain YB [auth K] mmCIF format, chain WA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain QC [auth R] mmCIF format, chain QB [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain MC [auth Q] mmCIF format, chain LC [auth Q] mmCIF format, chain KB [auth I] mmCIF format, chain GA [auth C] mmCIF format, chain EC [auth L] mmCIF format, chain DB [auth F] mmCIF format, chain CB [auth F]	CB [auth F] DB [auth F] EC [auth L] GA [auth C] KB [auth I] CB [auth F], DB [auth F], EC [auth L], GA [auth C], KB [auth I], LC [auth Q], MC [auth Q], NA [auth D], Q [auth A], QB [auth J], QC [auth R], W [auth B], WA [auth E], YB [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EC [auth L] Focus chain GA [auth C] Focus chain KB [auth I] Focus chain LC [auth Q] Focus chain MC [auth Q] Focus chain NA [auth D] Focus chain Q [auth A] Focus chain QB [auth J] Focus chain QC [auth R] Focus chain W [auth B] Focus chain WA [auth E] Focus chain YB [auth K] Interactions & Density Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EC [auth L] Focus chain GA [auth C] Focus chain KB [auth I] Focus chain LC [auth Q] Focus chain MC [auth Q] Focus chain NA [auth D] Focus chain Q [auth A] Focus chain QB [auth J] Focus chain QC [auth R] Focus chain W [auth B] Focus chain WA [auth E] Focus chain YB [auth K]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth E] SDF format, chain YA [auth E] SDF format, chain XB [auth K] SDF format, chain TC [auth R] SDF format, chain RC [auth R] SDF format, chain R [auth A] SDF format, chain PA [auth D] SDF format, chain HC [auth L] SDF format, chain BA [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain XB [auth K] MOL2 format, chain TC [auth R] MOL2 format, chain RC [auth R] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain HC [auth L] MOL2 format, chain BA [auth B] mmCIF format, chain ZA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain XB [auth K] mmCIF format, chain TC [auth R] mmCIF format, chain RC [auth R] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain HC [auth L] mmCIF format, chain BA [auth B]	BA [auth B] HC [auth L] PA [auth D] R [auth A] RC [auth R] BA [auth B], HC [auth L], PA [auth D], R [auth A], RC [auth R], TC [auth R], XB [auth K], YA [auth E], ZA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain HC [auth L] Focus chain PA [auth D] Focus chain R [auth A] Focus chain RC [auth R] Focus chain TC [auth R] Focus chain XB [auth K] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain BA [auth B] Focus chain HC [auth L] Focus chain PA [auth D] Focus chain R [auth A] Focus chain RC [auth R] Focus chain TC [auth R] Focus chain XB [auth K] Focus chain YA [auth E] Focus chain ZA [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain P [auth A] SDF format, chain MA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain P [auth A] MOL2 format, chain MA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain P [auth A] mmCIF format, chain MA [auth D]	MA [auth D] P [auth A] S [auth A] V [auth B] Y [auth B] MA [auth D], P [auth A], S [auth A], V [auth B], Y [auth B], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain MA [auth D] Focus chain P [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain MA [auth D] Focus chain P [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.245 (Depositor), 0.250 (DCC)
R-Value Work: 0.202 (Depositor), 0.209 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.61	α = 90
b = 70.015	β = 103.29
c = 131.544	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations