4CUK | pdb_00004cuk

Structure of Salmonella D-Lactate Dehydrogenase in complex with NADH

PDB DOI: https://doi.org/10.2210/pdb4CUK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-03-19 Released: 2015-05-27
Deposition Author(s): Attarataya, J., Zaccai, N.R., Brady, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.224 (Depositor), 0.233 (DCC)
R-Value Work:
0.177 (Depositor), 0.196 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

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

Literature

The Structure of Salmonella D-Lactate Dehydrogenase

Attarataya, J., Zaccai, N.R., Shoemark, D.K., Brady, R.L.

To be published.

Macromolecule Content

Total Structure Weight: 152.09 kDa
Atom Count: 10,931
Modeled Residue Count: 1,330
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-LACTATE DEHYDROGENASE	A, B, C, D	338	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0 EC: 1.1.1.28
UniProt
Find proteins for Q8Z780 (Salmonella typhi) Explore Q8Z780 Go to UniProtKB: Q8Z780
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Z780
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth D]	E [auth A], F [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.224 (Depositor), 0.233 (DCC)
R-Value Work: 0.177 (Depositor), 0.196 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.35	α = 90
b = 60.7	β = 106.92
c = 130.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.