2YZM | pdb_00002yzm

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2YZM/pdb

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

Deposited: 2007-05-06 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: 2.21 Å
R-Value Free:
0.266 (Depositor), 0.265 (DCC)
R-Value Work:
0.224 (Depositor), 0.224 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

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

To be published.

Macromolecule Content

Total Structure Weight: 104.37 kDa
Atom Count: 7,476
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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAL Query on DAL Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	D-ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-UWTATZPHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.266 (Depositor), 0.265 (DCC)
R-Value Work: 0.224 (Depositor), 0.224 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.705	α = 90
b = 55.849	β = 109.34
c = 141.387	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-10-25
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.