5VG3 | pdb_00005vg3

Structure of Oxalate Decarboxylase from Bacillus subtilis at pH 4.6

PDB DOI: https://doi.org/10.2210/pdb5VG3/pdb

Classification: LYASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-10 Released: 2017-10-18
Deposition Author(s): Angerhofer, A., Burg, M.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.177 (Depositor), 0.180 (DCC)
R-Value Work:
0.154 (Depositor), 0.150 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Oxalate Decarboxylase from Bacillus subtilis at pH 4.6

Angerhofer, A., Burg, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 131.57 kDa
Atom Count: 10,785
Modeled Residue Count: 1,135
Deposited Residue Count: 1,146
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxalate decarboxylase	A, B, C	382	Bacillus subtilis	Mutation(s): 0 Gene Names: B4417_3145 EC: 4.1.1.2
UniProt
Find proteins for O34714 (Bacillus subtilis (strain 168)) Explore O34714 Go to UniProtKB: O34714
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34714
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	Y [auth C], Z [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	L [auth A], S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], W [auth C], X [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain N [auth A] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain M [auth A] SDF format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain M [auth A] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] M [auth A] N [auth A] U [auth B] AA [auth C], BA [auth C], M [auth A], N [auth A], U [auth B], V [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.177 (Depositor), 0.180 (DCC)
R-Value Work: 0.154 (Depositor), 0.150 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.484	α = 90
b = 156.657	β = 119.28
c = 79.574	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Angerhofer, A.

Burg, M.J.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1213440

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations