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- PDB-6mdf: Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalon... -

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Basic information

Entry
Database: PDB / ID: 6mdf
TitleMevalonate kinase from Methanosarcina mazei with 5-phosphomevalonate bound
ComponentsMevalonate kinase
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Mevalonate kinase, archaeal / Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily ...Mevalonate kinase, archaeal / Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PMV / Mevalonate kinase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsMiller, B.R. / Kung, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116029 United States
CitationJournal: PLoS ONE / Year: 2018
Title: Structural insight into substrate and product binding in an archaeal mevalonate kinase.
Authors: Miller, B.R. / Kung, Y.
History
DepositionSep 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mevalonate kinase
B: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,92817
Polymers63,2752
Non-polymers1,65315
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-32 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.970, 58.581, 190.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mevalonate kinase / MVK


Mass: 31637.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: mvk, MM_1762 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PW39, mevalonate kinase
#2: Chemical ChemComp-PMV / (3R)-3-HYDROXY-3-METHYL-5-(PHOSPHONOOXY)PENTANOIC ACID / PHOSPHOMEVALONATE


Mass: 228.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris, pH 5.5, 200-300 mM sodium potassium tartrate, 15-25% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2018
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.46→51.92 Å / Num. obs: 22260 / % possible obs: 96.95 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1031 / Net I/σ(I): 8.73
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3752 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 2135 / CC1/2: 0.843 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HAC

4hac


Resolution: 2.46→51.92 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.84
RfactorNum. reflection% reflection
Rfree0.2672 1158 5.21 %
Rwork0.2003 --
obs0.2038 22219 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.46→51.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 106 208 4639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034494
X-RAY DIFFRACTIONf_angle_d0.516083
X-RAY DIFFRACTIONf_dihedral_angle_d7.4373593
X-RAY DIFFRACTIONf_chiral_restr0.043732
X-RAY DIFFRACTIONf_plane_restr0.003777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.5720.34471490.25762547X-RAY DIFFRACTION96
2.572-2.70760.34251420.24372586X-RAY DIFFRACTION99
2.7076-2.87720.28851420.22592631X-RAY DIFFRACTION99
2.8772-3.09930.27411460.22352634X-RAY DIFFRACTION99
3.0993-3.41120.27971360.20472644X-RAY DIFFRACTION99
3.4112-3.90470.29051360.19142608X-RAY DIFFRACTION96
3.9047-4.91910.21111530.16152687X-RAY DIFFRACTION99
4.9191-55.99570.25951540.20082724X-RAY DIFFRACTION96

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