3E96

Crystal structure of dihydrodipicolinate synthase from bacillus clausii

PDB DOI: https://doi.org/10.2210/pdb3E96/pdb

Classification: LYASE
Organism(s): Shouchella clausii KSM-K16
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-21 Released: 2008-09-02
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.213
R-Value Work: 0.193
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of dihydrodipicolinate synthase from bacillus clausii

Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 70.51 kDa
Atom Count: 5,136
Modelled Residue Count: 596
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	316	Shouchella clausii KSM-K16	Mutation(s): 0 Gene Names: ABC3015 EC: 4.2.1.52
UniProt
Find proteins for Q5WDL1 (Shouchella clausii (strain KSM-K16)) Explore Q5WDL1 Go to UniProtKB: Q5WDL1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5WDL1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.213
R-Value Work: 0.193
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.766	α = 90
b = 80.938	β = 90
c = 93.166	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
Auto-Rickshaw	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-03-21
Changes: Structure summary
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-10
Changes: Database references, Structure summary
Version 1.6: 2024-02-21
Changes: Data collection, Database references

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.