4PIB | pdb_00004pib

Crystal Structure of Uncharacterized Conserved Protein PixA from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb4PIB/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-05-08 Released: 2014-07-02
Deposition Author(s): Kim, Y., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.181 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Uncharacterized Conserved Protein PixA from Burkholderia thailandensis

Kim, Y., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 211.2 kDa
Atom Count: 14,478
Modeled Residue Count: 1,749
Deposited Residue Count: 1,930
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
inclusion body protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	193	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: BTH_I2413
UniProt
Find proteins for Q2SVW5 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2SVW5 Go to UniProtKB: Q2SVW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2SVW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain ZA [auth H] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain UA [auth G] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain HA [auth D] SDF format, chain DB [auth I] MOL2 format, chain GA [auth D] MOL2 format, chain ZA [auth H] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain DB [auth I] mmCIF format, chain GA [auth D] mmCIF format, chain ZA [auth H] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain DB [auth I]	DB [auth I] GA [auth D] HA [auth D] O [auth A] P [auth A] DB [auth I], GA [auth D], HA [auth D], O [auth A], P [auth A], UA [auth G], V [auth B], W [auth B], ZA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DB [auth I] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain UA [auth G] Focus chain V [auth B] Focus chain W [auth B] Focus chain ZA [auth H] Interactions & Density Focus chain DB [auth I] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain UA [auth G] Focus chain V [auth B] Focus chain W [auth B] Focus chain ZA [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain BA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain BA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain BA [auth C]	BA [auth C], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain U [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain FB [auth J] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain Z [auth C] SDF format, chain YA [auth H] SDF format, chain Y [auth C] SDF format, chain XA [auth H] SDF format, chain VA [auth H] SDF format, chain TA [auth G] SDF format, chain T [auth B] SDF format, chain SA [auth G] SDF format, chain S [auth B] SDF format, chain RA [auth G] SDF format, chain OA [auth F] SDF format, chain NA [auth E] SDF format, chain N [auth A] SDF format, chain MA [auth E] SDF format, chain LA [auth E] SDF format, chain IA [auth E] SDF format, chain FA [auth D] SDF format, chain EB [auth J] SDF format, chain EA [auth D] SDF format, chain CB [auth I] SDF format, chain CA [auth D] SDF format, chain BB [auth I] SDF format, chain AB [auth I] SDF format, chain AA [auth C] MOL2 format, chain FB [auth J] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain VA [auth H] MOL2 format, chain TA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain OA [auth F] MOL2 format, chain NA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain CB [auth I] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain AB [auth I] MOL2 format, chain AA [auth C] mmCIF format, chain FB [auth J] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain VA [auth H] mmCIF format, chain TA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain OA [auth F] mmCIF format, chain NA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth J] mmCIF format, chain EA [auth D] mmCIF format, chain CB [auth I] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain AB [auth I] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth I] BB [auth I] CA [auth D] CB [auth I] AA [auth C], AB [auth I], BB [auth I], CA [auth D], CB [auth I], EA [auth D], EB [auth J], FA [auth D], FB [auth J], IA [auth E], JA [auth E], K [auth A], LA [auth E], M [auth A], MA [auth E], N [auth A], NA [auth E], OA [auth F], PA [auth F], Q [auth B], RA [auth G], S [auth B], SA [auth G], T [auth B], TA [auth G], VA [auth H], X [auth C], XA [auth H], Y [auth C], YA [auth H], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth D] Focus chain FB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth G] Focus chain VA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth D] Focus chain FB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth G] Focus chain VA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain WA [auth H] SDF format, chain QA [auth F] SDF format, chain L [auth A] SDF format, chain KA [auth E] SDF format, chain GB [auth J] SDF format, chain DA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain QA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain GB [auth J] MOL2 format, chain DA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain QA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain GB [auth J] mmCIF format, chain DA [auth D]	DA [auth D] GB [auth J] KA [auth E] L [auth A] QA [auth F] DA [auth D], GB [auth J], KA [auth E], L [auth A], QA [auth F], R [auth B], WA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain GB [auth J] Focus chain KA [auth E] Focus chain L [auth A] Focus chain QA [auth F] Focus chain R [auth B] Focus chain WA [auth H] Interactions & Density Focus chain DA [auth D] Focus chain GB [auth J] Focus chain KA [auth E] Focus chain L [auth A] Focus chain QA [auth F] Focus chain R [auth B] Focus chain WA [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.181 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.806	α = 90
b = 84.868	β = 90
c = 249.693	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	phasing
RESOLVE	model building
PHENIX	phasing
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-07-02
Type: Initial release
Version 1.1: 2017-11-22
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary