8I78 | pdb_00008i78

Meso-Diaminopimelate dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb8I78/pdb

Classification: OXIDOREDUCTASE
Organism(s): Proteus vulgaris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-31 Released: 2024-02-07
Deposition Author(s): Wei, S., Wu, T.F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.214 (Depositor), 0.232 (DCC)
R-Value Work:
0.183 (Depositor), 0.200 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Analysis of the catalytic mechanism of meso-DAPDH and extension of D-aromatic amino acid substrate scope

wu, T.F., wei, S.

To be published.

Macromolecule Content

Total Structure Weight: 129.1 kDa
Atom Count: 9,445
Modeled Residue Count: 1,188
Deposited Residue Count: 1,196
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meso-diaminopimelate D-dehydrogenase	A, B, C, D	299	Proteus vulgaris	Mutation(s): 0 Gene Names: EKQ45_05540 EC: 1.4.1.16
UniProt
Find proteins for A0A379F6K8 (Proteus vulgaris) Explore A0A379F6K8 Go to UniProtKB: A0A379F6K8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A379F6K8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.214 (Depositor), 0.232 (DCC)
R-Value Work: 0.183 (Depositor), 0.200 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.91	α = 90
b = 211.91	β = 90
c = 245.76	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release

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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.