1WZI | pdb_00001wzi

Structural basis for alteration of cofactor specificity of Malate dehydrogenase from Thermus flavus

PDB DOI: https://doi.org/10.2210/pdb1WZI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-03-05 Released: 2006-03-14
Deposition Author(s): Tomita, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.229 (Depositor), 0.183 (DCC)
R-Value Work:
0.196 (Depositor), 0.191 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural basis for alteration of cofactor specificity of malate dehydrogenase from Thermus flavus

Tomita, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

To be published.

Macromolecule Content

Total Structure Weight: 72.41 kDa
Atom Count: 5,682
Modeled Residue Count: 654
Deposited Residue Count: 654
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	327	Thermus thermophilus	Mutation(s): 7 Gene Names: mdh EC: 1.1.1.37
UniProt
Find proteins for P10584 (Thermus thermophilus) Explore P10584 Go to UniProtKB: P10584
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10584
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.229 (Depositor), 0.183 (DCC)
R-Value Work: 0.196 (Depositor), 0.191 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.31	α = 90
b = 85.39	β = 90
c = 117.7	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-03-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-11-29
Changes: Derived calculations
Version 1.4: 2021-11-10
Changes: Database references, Derived calculations
Version 1.5: 2023-10-25
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.