2FB9

Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes

PDB DOI: https://doi.org/10.2210/pdb2FB9/pdb

Classification: LIGASE
Organism(s): Thermus caldophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-12-08 Released: 2006-08-29
Deposition Author(s): Lee, J.H., Na, Y., Eom, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.268
R-Value Work: 0.228
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes

Lee, J.H., Na, Y., Song, H.E., Kim, D., Park, B.H., Rho, S.H., Im, Y.J., Kim, M.K., Kang, G.B., Lee, D.S., Eom, S.H.

(2006) Proteins 64: 1078-1082

PubMed: 16779845 Search on PubMed
DOI: https://doi.org/10.1002/prot.20927
Primary Citation of Related Structures:
2FB9

Organizational Affiliation

Department of Life Science, Gwangju Institute of Science & Technology, Gwangju, Korea.

Macromolecule Content

Total Structure Weight: 35.11 kDa
Atom Count: 2,596
Modelled Residue Count: 322
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine:D-alanine ligase	A	322	Thermus caldophilus	Mutation(s): 0 EC: 6.3.2.4
UniProt
Find proteins for Q3T920 (Thermus caldophilus) Explore Q3T920 Go to UniProtKB: Q3T920
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3T920
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.268
R-Value Work: 0.228
R-Value Observed: 0.232
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.216	α = 90
b = 132.744	β = 90
c = 59.324	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-08-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.