3WGO | pdb_00003wgo

Crystal structure of Q154L/T173I/R199M/P248S/H249/N276S mutant of meso-dapdh from Clostridium tetani E88

PDB DOI: https://doi.org/10.2210/pdb3WGO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium tetani E88
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-08-06 Released: 2014-08-20
Deposition Author(s): Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Q154L/T173I/R199M/P248S/H249 mutant of meso-dapdh from Clostridium tetani E88

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 72.57 kDa
Atom Count: 5,837
Modelled Residue Count: 647
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meso-diaminopimelate dehydrogenase	A, B	326	Clostridium tetani E88	Mutation(s): 6 Gene Names: CTC_02532, meso-dapdh EC: 1.4.1.16
UniProt
Find proteins for Q890V3 (Clostridium tetani (strain Massachusetts / E88)) Explore Q890V3 Go to UniProtKB: Q890V3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q890V3
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.260 (Depositor), 0.260 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.13	α = 90
b = 135.619	β = 110.46
c = 60.67	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-08-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-20
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, 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.