7ARZ | pdb_00007arz

Ternary complex of NAD-dependent formate dehydrogenase from Physcomitrium patens

PDB DOI: https://doi.org/10.2210/pdb7ARZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Physcomitrium patens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-26 Released: 2021-11-03
Deposition Author(s): Goryaynova, D.A., Nikolaeva, A.Y., Pometun, A.A., Savin, S.S., Parshin, P.D., Popov, V.O., Tishkov, V.I., Boyko, K.M.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.257 (Depositor), 0.264 (DCC)
R-Value Work:
0.206 (Depositor), 0.214 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Ternary complex of NAD-dependent formate dehydrogenase from Physcomitrium patens

Boyko, K.M., Pometun, A.A., Goryaynova, D.A., Nikolaeva, A.Y., Parshin, P.D., Popov, V.O., Tishkov, V.I.

To be published.

Macromolecule Content

Total Structure Weight: 40.47 kDa
Atom Count: 2,975
Modeled Residue Count: 361
Deposited Residue Count: 361
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, mitochondrial	A	361	Physcomitrium patens	Mutation(s): 0 Gene Names: PHYPA_020821, PHYPADRAFT_214795 EC: 1.17.1.9
UniProt
Find proteins for A9SQZ2 (Physcomitrium patens) Explore A9SQZ2 Go to UniProtKB: A9SQZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9SQZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
AZI (Subject of Investigation/LOI) Query on AZI Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.257 (Depositor), 0.264 (DCC)
R-Value Work: 0.206 (Depositor), 0.214 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.36	α = 90
b = 68.36	β = 90
c = 203.44	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Goryaynova, D.A.

Nikolaeva, A.Y.

Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	18-34-20098

Revision History (Full details and data files)

Version 1.0: 2021-11-03
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.