7RRL

Alternate Crystal Form of Human Malate Dehydrogenase I

PDB DOI: https://doi.org/10.2210/pdb7RRL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-09 Released: 2022-02-16
Deposition Author(s): McCue, W., Finzel, B.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.237
R-Value Work: 0.186
R-Value Observed: 0.189

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural Studies to Enable Drug Discovery

(2021) Ph D Thesis,university Of Minnesota

Macromolecule Content

Total Structure Weight: 72.94 kDa
Atom Count: 5,057
Modelled Residue Count: 655
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase, cytoplasmic	A, B	334	Homo sapiens	Mutation(s): 0 Gene Names: MDH1, MDHA EC: 1.1.1.37 (PDB Primary Data), 1.1.1.96 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P40925 (Homo sapiens) Explore P40925 Go to UniProtKB: P40925
PHAROS: P40925 GTEx: ENSG00000014641
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40925
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.237
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.875	α = 90
b = 62.593	β = 91.219
c = 74.322	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
JDirector	data collection
PHASER	phasing
AutoProcess	data processing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-02-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-02-16
Type: Initial release
Version 1.1: 2023-10-18
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.