6IQV

Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with Hg2+ from Lactobacillus plantarum

PDB DOI: https://doi.org/10.2210/pdb6IQV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-11-09 Released: 2018-11-21
Deposition Author(s): Yoneda, K., Kinoshita, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.229
R-Value Work: 0.202
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase from Lactobacillus plantarum: Insight into the Mercury Binding Mechanism

Yoneda, K., Ogata, M., Nishiyama, K., Fukuda, K., Yasuda, S., Igoshi, K., Kinoshita, H.

(2019) Milk Sci 68: 3-11

DOI: https://doi.org/10.11465/milk.68.3

Macromolecule Content

Total Structure Weight: 148.61 kDa
Atom Count: 10,725
Modelled Residue Count: 1,335
Deposited Residue Count: 1,360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase, type I	A, B, C, D	340	Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437	Mutation(s): 0 Gene Names: gap, HMPREF0531_11006 EC: 1.2.1.12
UniProt
Find proteins for D7VA33 (Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437) Explore D7VA33 Go to UniProtKB: D7VA33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D7VA33
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], S [auth D], T [auth D], U [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth D]	E [auth A] I [auth A] K [auth B] O [auth C] R [auth D] E [auth A], I [auth A], K [auth B], O [auth C], R [auth D], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.229
R-Value Work: 0.202
R-Value Observed: 0.205
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.043	α = 90
b = 172.949	β = 90
c = 149.235	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Yoneda, K.

Kinoshita, H.

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2019-05-15
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description