2YZG | pdb_00002yzg

Crystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2YZG/pdb

Classification: LIGASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-05 Released: 2007-11-06
Deposition Author(s): Kitamura, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.290 (Depositor), 0.288 (DCC)
R-Value Work:
0.243 (Depositor), 0.242 (DCC)
R-Value Observed:
0.243 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2YZG

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

Literature

Crystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8

Kitamura, Y., Yokoyama, S., Kuramitsu, S.

To be published.

Macromolecule Content

Total Structure Weight: 104.66 kDa
Atom Count: 7,393
Modeled Residue Count: 939
Deposited Residue Count: 957
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase	A, B, C	319	Thermus thermophilus HB8	Mutation(s): 0 EC: 6.3.2.4
UniProt
Find proteins for Q5SHZ3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ3 Go to UniProtKB: Q5SHZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.290 (Depositor), 0.288 (DCC)
R-Value Work: 0.243 (Depositor), 0.242 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.224	α = 90
b = 56.412	β = 109.08
c = 142.213	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-11-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.