6TTB | pdb_00006ttb

Crystal structure of NAD-dependent formate dehydrogenase from Staphylococcus aureus in complex with NAD

PDB DOI: https://doi.org/10.2210/pdb6TTB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-12-26 Released: 2021-01-13
Deposition Author(s): Boyko, K.M., Pometun, A.A., Nikolaeva, A.Y., Kargov, I.S., Yurchenko, T.S., Savin, S.S., Popov, V.O., Tishkov, V.I.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of NAD-dependent formate dehydrogenase from Staphylococcus aureus in complex with NAD

Boyko, K.M., Pometun, A.A., Nikolaeva, A.Y., Kargov, I.S., Yurchenko, T.S., Savin, S.S., Tishkov, V.I.

To be published.

Macromolecule Content

Total Structure Weight: 84.37 kDa
Atom Count: 5,096
Modeled Residue Count: 658
Deposited Residue Count: 746
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B	373	Staphylococcus aureus	Mutation(s): 0 Gene Names: M1K003_0593 EC: 1.17.1.9 (UniProt), 1.1.1.28 (UniProt)
UniProt
Find proteins for A0A0H3JSR9 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JSR9 Go to UniProtKB: A0A0H3JSR9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3JSR9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.182 (Depositor), 0.183 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.29	α = 90
b = 87.36	β = 90
c = 117.63	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-13

Deposition Author(s):

Nikolaeva, A.Y.

Yurchenko, T.S.

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	14-24-00172

Revision History (Full details and data files)

Version 1.0: 2021-01-13
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, 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.