3FMX | pdb_00003fmx

Crystal structure of Tartrate dehydrogenase from Pseudomonas putida complexed with NADH

PDB DOI: https://doi.org/10.2210/pdb3FMX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-12-22 Released: 2010-01-12
Deposition Author(s): Malik, R., Viola, R.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.297 (Depositor), 0.310 (DCC)
R-Value Work:
0.260 (Depositor), 0.260 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Characterization of Tartrate Dehydrogenase: a versatile enzyme catalyzing multiple reactions

Malik, R., Viola, R.E.

To be published.

Macromolecule Content

Total Structure Weight: 41.2 kDa
Atom Count: 2,875
Modeled Residue Count: 359
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tartrate dehydrogenase/decarboxylase	A [auth X]	364	Pseudomonas putida	Mutation(s): 1 Gene Names: ttuC EC: 1.1.1.93 (PDB Primary Data), 4.1.1.73 (PDB Primary Data), 1.1.1.83 (PDB Primary Data)
UniProt
Find proteins for Q51945 (Pseudomonas putida) Explore Q51945 Go to UniProtKB: Q51945
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q51945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.297 (Depositor), 0.310 (DCC)
R-Value Work: 0.260 (Depositor), 0.260 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.906	α = 90
b = 182.906	β = 90
c = 66.98	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-11-06
Changes: Non-polymer description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description

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.