3CM0 | pdb_00003cm0

Crystal structure of adenylate kinase from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb3CM0/pdb

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

Deposited: 2008-03-20 Released: 2008-09-23
Deposition Author(s): Nakagawa, N., Kondo, N., Masui, R., Matsuda, Z., Iwamoto, I., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.242 (Depositor), 0.212 (DCC)
R-Value Work:
0.205 (Depositor), 0.209 (DCC)
R-Value Observed:
0.205 (Depositor)

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

Literature

Crystal structure of adenylate kinase from Thermus thermophilus HB8.

Nakagawa, N., Kondo, N., Masui, R., Yokoyama, S., Kuramitsu, S.

To be published.

Macromolecule Content

Total Structure Weight: 20.78 kDa
Atom Count: 1,533
Modeled Residue Count: 184
Deposited Residue Count: 186
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A	186	Thermus thermophilus	Mutation(s): 0 Gene Names: adk EC: 2.7.4.3
UniProt
Find proteins for Q5SHQ9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ9 Go to UniProtKB: Q5SHQ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHQ9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.242 (Depositor), 0.212 (DCC)
R-Value Work: 0.205 (Depositor), 0.209 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.446	α = 90
b = 51.446	β = 90
c = 131.474	γ = 120

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: 2008-09-23

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-09-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-08-14
Changes: Database references

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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.