3WGZ | pdb_00003wgz

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with D-leucine of from Clostridium tetani E88

PDB DOI: https://doi.org/10.2210/pdb3WGZ/pdb

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

Deposited: 2013-08-20 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: 2.25 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with D-leucine of 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: 72.7 kDa
Atom Count: 5,571
Modeled Residue Count: 647
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q890V3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DLE Query on DLE Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	D-LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-RXMQYKEDSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.263 (Depositor), 0.262 (DCC)
R-Value Work: 0.206 (Depositor), 0.206 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.727	α = 90
b = 136.072	β = 110.28
c = 60.051	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection

Structure Validation

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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, Derived calculations, 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.