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- PDB-36wi: Mevalonate kinase from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 36wi
TitleMevalonate kinase from Saccharomyces cerevisiae
ComponentsMevalonate kinase
KeywordsTRANSFERASE / metabolic enzyme / mevalonate pathway
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / Lanosterol biosynthesis / ergosterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / farnesyl diphosphate biosynthetic process, mevalonate pathway / magnesium ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsD'Emilia, R.L.S. / Ragwan, E.R. / Tang, M.M. / Chang, V. / 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: J.Biol.Chem. / Year: 2026
Title: Structural basis of mevalonate pathway regulation by feedback inhibition of mevalonate kinase.
Authors: D'Emilia, R.L.S. / McCaskey, K.A. / Ragwan, E.R. / Kim, J.H. / Chang, V. / Tang, M.M. / Kung, Y.
History
DepositionJul 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7745
Polymers51,4951
Non-polymers2784
Water2,180121
1
A: Mevalonate kinase
hetero molecules

A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,54710
Polymers102,9912
Non-polymers5578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4410 Å2
ΔGint2 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.450, 83.450, 262.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Mevalonate kinase / MK / MvK / Ergosterol biosynthesis protein 12 / Regulation of autonomous replication protein 1


Mass: 51495.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERG12, RAR1, YMR208W, YM8261.02 / Production host: Escherichia coli (E. coli) / References: UniProt: P07277, mevalonate kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 4.44 Å3/Da / Density % sol: 72.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6.0, 900-1100 mM sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→83.45 Å / Num. obs: 49876 / % possible obs: 97.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.53 Å2 / CC1/2: 0.995 / Net I/σ(I): 5.9
Reflection shellResolution: 2.15→2.21 Å / Num. unique obs: 738 / CC1/2: 0.305 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→79.54 Å / SU ML: 0.3178 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 2490 5 %
Rwork0.1982 47314 -
obs0.1995 49804 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.12 Å2
Refinement stepCycle: LAST / Resolution: 2.15→79.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 18 121 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693523
X-RAY DIFFRACTIONf_angle_d0.94414773
X-RAY DIFFRACTIONf_chiral_restr0.0491558
X-RAY DIFFRACTIONf_plane_restr0.0067613
X-RAY DIFFRACTIONf_dihedral_angle_d14.53891272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.39691380.38422620X-RAY DIFFRACTION98.25
2.19-2.240.37141380.35032602X-RAY DIFFRACTION98.28
2.24-2.280.33951380.3372618X-RAY DIFFRACTION97.83
2.28-2.340.32061370.31982622X-RAY DIFFRACTION97.98
2.34-2.40.31541390.31232631X-RAY DIFFRACTION97.64
2.4-2.460.3121380.29882627X-RAY DIFFRACTION97.63
2.46-2.530.28731340.26212573X-RAY DIFFRACTION95.86
2.53-2.620.27381370.23422605X-RAY DIFFRACTION97.55
2.62-2.710.27661400.22542640X-RAY DIFFRACTION97.51
2.71-2.820.24471370.21972621X-RAY DIFFRACTION97.46
2.82-2.950.24331370.21812620X-RAY DIFFRACTION96.87
2.95-3.10.25231400.21752647X-RAY DIFFRACTION96.44
3.1-3.30.21481360.18892581X-RAY DIFFRACTION95.77
3.3-3.550.19661380.18162618X-RAY DIFFRACTION95.59
3.55-3.910.19871360.16132591X-RAY DIFFRACTION94.13
3.91-4.470.15791400.14072650X-RAY DIFFRACTION95.71
4.47-5.630.18471420.15472701X-RAY DIFFRACTION95.05
5.64-79.540.19681450.17322747X-RAY DIFFRACTION91.52
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.048331424410.1908728425370.9330779917820.447350200240.3845248791521.21953401683-0.01463428603650.146507889684-0.0960865283404-0.04881784179580.105193235425-0.02919713135580.004621752950650.136753630334-7.53964280781E-100.313586549997-0.0175163905250.0003632751442410.463932179166-0.05817410974450.371922741538-4.17182514972-24.039301404330.3555858347
2-0.00302779591831-0.0365352156526-0.008858193831010.067893639584-0.02133647745310.06959978590670.04748908630570.315862916325-0.1822620739490.1015760074750.10027606263-0.1811522498290.1667546261110.339780896073-3.63168877539E-70.454029813166-0.0100629024827-0.06518153052210.555403402188-0.06981529773430.491937761597.6833091751-27.799510223745.6221501712
30.8646845034650.03435146540050.496758577630.6730297832850.2367634664481.100222811570.0701250300659-0.0608805753515-0.05224913855670.0676799947765-0.05073322391620.07087159601790.058550300628-0.224092284492-5.97873791947E-90.299564883020.0311395819201-0.005969127853850.344567862312-0.02480988463260.3493646435630.702987155812-16.116492548360.5683924171
40.3511466942780.0297538148655-0.03644997725570.1870076587770.2071583722530.238941261127-0.0629239094776-0.553057319395-0.006700715311950.1672538410360.02715010785110.136465231753-0.11221752971-0.21179410694-1.59967151718E-90.375963502221-0.005016927215980.004107445503530.628764330527-0.03113531456980.4649879963-21.3287970724-23.164253247640.2041034726
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -7 through 195 )-7 - 1951 - 203
22chain 'A' and (resid 196 through 227 )196 - 227204 - 235
33chain 'A' and (resid 228 through 391 )228 - 391236 - 399
44chain 'A' and (resid 392 through 443 )392 - 443400 - 451

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