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), 0.306 (DCC)
R-Value Work:
0.260 (Depositor), 0.259 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.306 (DCC)
R-Value Work: 0.260 (Depositor), 0.259 (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

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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

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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.