6L9I | pdb_00006l9i

Crystal Structure of Lactobacillus farciminis Oxalate Decarboxylase Formate Complex

PDB DOI: https://doi.org/10.2210/pdb6L9I/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Companilactobacillus farciminis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-10 Released: 2021-01-20
Deposition Author(s): Wu, F., Cheng, L.K., Wang, C.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.229 (Depositor), 0.212 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Lactobacillus farciminis Oxalate Decarboxylase Formate Complex

Wu, F., Cheng, L.K., Wang, C.Y.

To be published.

Macromolecule Content

Total Structure Weight: 244.36 kDa
Atom Count: 16,298
Modeled Residue Count: 2,028
Deposited Residue Count: 2,160
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxalate decarboxylase	A, B, C, D, E A, B, C, D, E, F	360	Companilactobacillus farciminis	Mutation(s): 0 Gene Names: ABB44_10110, ABB45_10090

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] L [auth B] N [auth C] H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], Q [auth D], R [auth D], T [auth E], U [auth E], W [auth F], X [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F]
FMT (Subject of Investigation/LOI) Query on FMT Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain S [auth E] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] M [auth C] P [auth D] S [auth E] G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.229 (Depositor), 0.212 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.957	α = 90
b = 122.842	β = 92.475
c = 115.223	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-20

Deposition Author(s):

Wu, F.

Cheng, L.K.

Wang, C.Y.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31700625

Revision History (Full details and data files)

Version 1.0: 2021-01-20
Type: Initial release
Version 1.1: 2023-11-22
Changes: Advisory, Data collection, Database references, Refinement description