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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.242 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of adenylate kinase from Thermus thermophilus HB8.

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.242 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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