3W8N | pdb_00003w8n

Open form structure of CMP kinase in complex with CMP from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb3W8N/pdb

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


• Deposited: 2013-03-19 Released: 2013-09-25 
• Deposition Author(s): Nakagawa, N., Mega, R., Masui, R., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.202 (DCC) 

Literature

Crystal structure of CMP kinase: insights into initial substrate recognition and reaction mechanisms

Mega, R., Nakagawa, N., Masui, R., 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: 23.05 kDa 
• Atom Count: 1,623 
• Modeled Residue Count: 201 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidylate kinase	A	208	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0458 EC: 2.7.4.25
UniProt
Find proteins for Q5SL35 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL35  Go to UniProtKB:  Q5SL35

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C5P	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.202 (DCC) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.212	α = 90
b = 49.212	β = 90
c = 98.051	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Nakagawa, N., Mega, R., Masui, R., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary