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- PDB-3ch4: The Crystal Structure of Human Phosphomavelonate Kinase At 1.8 A ... -

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Basic information

Entry
Database: PDB / ID: 3ch4
TitleThe Crystal Structure of Human Phosphomavelonate Kinase At 1.8 A Resolution
ComponentsPhosphomevalonate kinase
KeywordsTRANSFERASE / parallel beta-sheet with the strand order 23145 / Walker A motif / Cholesterol biosynthesis / Kinase / Lipid synthesis / Peroxisome / Steroid biosynthesis / Sterol biosynthesis
Function / homology
Function and homology information


phosphomevalonate kinase activity / phosphomevalonate kinase / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / Cholesterol biosynthesis / response to cholesterol / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome ...phosphomevalonate kinase activity / phosphomevalonate kinase / regulation of cholesterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / Cholesterol biosynthesis / response to cholesterol / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome / extracellular exosome / ATP binding / membrane / cytosol
Similarity search - Function
Higher eukaryotic phosphomevalonate kinase / Phosphomevalonate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphomevalonate kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.76 Å
AuthorsLiang, D.-C. / Chang, Q. / Yan, X.-X. / Gu, S.-Y.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of human phosphomavelonate kinase at 1.8 A resolution
Authors: Chang, Q. / Yan, X.-X. / Gu, S.-Y. / Liu, J.-F. / Liang, D.-C.
History
DepositionMar 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Phosphomevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6675
Polymers23,2381
Non-polymers4284
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.140, 32.625, 61.786
Angle α, β, γ (deg.)90.00, 111.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphomevalonate kinase / / PMKase


Mass: 23238.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q15126, phosphomevalonate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.89 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 15-20% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH), 15% (v/v) MPD, 0.1M Hepes, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 29, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→8 Å / Num. all: 17293 / Num. obs: 16987 / % possible obs: 99.4 % / Observed criterion σ(F): 4.1 / Observed criterion σ(I): 3 / Redundancy: 9.8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.9
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1598 / % possible all: 98.2

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Processing

Software
NameClassification
MAR345dtbdata collection
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→8 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 1698 RANDOM
Rwork0.199 --
all0.209 17293 -
obs0.199 16987 -
Refinement stepCycle: LAST / Resolution: 1.76→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 10 164 1689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.523
X-RAY DIFFRACTIONc_dihedral_angle_d23.178
X-RAY DIFFRACTIONc_improper_angle_d0.851
LS refinement shellResolution: 1.76→1.8 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.221 1698 -
Rwork0.199 --
obs-16987 98 %

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