1J5P | pdb_00001j5p

Crystal structure of aspartate dehydrogenase (TM1643) from Thermotoga maritima at 1.9 A resolution

PDB DOI: https://doi.org/10.2210/pdb1J5P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-06-27 Released: 2002-07-10
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.260 (Depositor), 0.256 (DCC)
R-Value Work:
0.224 (Depositor), 0.221 (DCC)
R-Value Observed:
0.224 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of aspartate dehydrogenase (TM1643) from Thermotoga maritima at 1.9 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 28.8 kDa
Atom Count: 1,964
Modeled Residue Count: 235
Deposited Residue Count: 253
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE DEHYDROGENASE	A	253	Thermotoga maritima	Mutation(s): 0 Gene Names: TM1643 EC: 1.4.3.16 (PDB Primary Data), 1.4.1.21 (UniProt)
UniProt
Find proteins for Q9X1X6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1X6 Go to UniProtKB: Q9X1X6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1X6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.260 (Depositor), 0.256 (DCC)
R-Value Work: 0.224 (Depositor), 0.221 (DCC)
R-Value Observed: 0.224 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.2	α = 90
b = 63.2	β = 90
c = 126.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
CCP4	data reduction
SOLVE	phasing
RESOLVE	model building
CNS	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-07-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2002-07-10
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2018-07-18
Changes: Advisory, Data collection, Database references
Version 1.4: 2023-01-25
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2024-05-22
Changes: Data collection

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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.