4HAC

Crystal Structure of the Mevalonate Kinase from an Archaeon Methanosarcina mazei

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


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


Literature

Crystallization and preliminary X-ray diffraction analysis of mevalonate kinase from Methanosarcina mazei.

Zhuang, N., Seo, K.H., Chen, C., Zhou, J., Kim, S.W., Lee, K.H.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1560-1563

  • DOI: 10.1107/S1744309112047070
  • Primary Citation of Related Structures:  
    4HAC

  • PubMed Abstract: 

    • Mevalonate kinase (MVK), which plays an important role in catalysing the biosynthesis of isoprenoid compounds derived from the mevalonate pathway, transforms mevalonate to 5-phosphomevalonate using ATP as a cofactor. Mevalonate kinase from Methanosar ...

    Mevalonate kinase (MVK), which plays an important role in catalysing the biosynthesis of isoprenoid compounds derived from the mevalonate pathway, transforms mevalonate to 5-phosphomevalonate using ATP as a cofactor. Mevalonate kinase from Methanosarcina mazei (MmMVK) was expressed in Escherichia coli, purified and crystallized for structural analysis. Diffraction-quality crystals of MmMVK were obtained by the vapour-diffusion method using 0.32 M MgCl2, 0.08 M bis-tris pH 5.5, 16%(w/v) PEG 3350. The crystals belonged to space group P2(1)2(1)2, with unit-cell parameters a=97.11, b=135.92, c=46.03 Å. Diffraction data were collected to 2.08 Å resolution.

    Organizational Affiliation: 

    Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju 660-701, Republic of Korea.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mevalonate kinaseA321Methanosarcina mazei Go1Mutation(s): 0 
Gene Names: MM_1762, mvk
EC: 2.7.1.36
Find proteins for Q8PW39 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PW39 
Go to UniProtKB:  Q8PW39
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mevalonate kinaseB321Methanosarcina mazei Go1Mutation(s): 0 
Gene Names: MM_1762, mvk
EC: 2.7.1.36
Find proteins for Q8PW39 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PW39 
Go to UniProtKB:  Q8PW39
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.295α = 90
b = 135.359β = 90
c = 45.867γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-09-26 
  • Released Date: 2012-12-12 
    • Deposition Author(s): Zhuang, N., Lee, K.H.

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description