Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 67.7 kDa 
• Atom Count: 4,710 
• Modelled Residue Count: 620 
• Deposited Residue Count: 642 
• Unique protein chains: 2

 4HAC

Crystal Structure of the Mevalonate Kinase from an Archaeon Methanosarcina mazei

• PDB DOI: 10.2210/pdb4HAC/pdb

• Classification: TRANSFERASE
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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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 

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

• PubMed: 23192048 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mevalonate kinase	A	321	Methanosarcina mazei Go1	Mutation(s): 0  Gene Names: MM_1762, mvk EC: 2.7.1.36
UniProt
Find proteins for Q8PW39 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PW39  Go to UniProtKB:  Q8PW39

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mevalonate kinase	B	321	Methanosarcina mazei Go1	Mutation(s): 0  Gene Names: MM_1762, mvk EC: 2.7.1.36
UniProt
Find proteins for Q8PW39 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PW39  Go to UniProtKB:  Q8PW39

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-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: 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 = 97.295	α = 90
b = 135.359	β = 90
c = 45.867	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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