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- PDB-8tfo: Structure of MKvar -

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Basic information

Entry
Database: PDB / ID: 8tfo
TitleStructure of MKvar
ComponentsMevalonate kinase
KeywordsTRANSFERASE / extremo-tolerant / psychrophilic
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Mevalonate kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / 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
(R)-MEVALONATE / DI(HYDROXYETHYL)ETHER / Mevalonate kinase
Similarity search - Component
Biological speciesRamazzottius varieornatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPeat, T.S. / Newman, J. / Esquirol, L. / Nebl, T. / Scott, C. / Vickers, C. / Sainsbury, F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii.
Authors: Esquirol, L. / Newman, J. / Nebl, T. / Scott, C. / Vickers, C. / Sainsbury, F. / Peat, T.S.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: 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
B: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2267
Polymers90,6802
Non-polymers5475
Water2,720151
1
A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5933
Polymers45,3401
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6334
Polymers45,3401
Non-polymers2933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.081, 80.705, 207.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 405 / Label seq-ID: 10 - 414

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Mevalonate kinase


Mass: 45339.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramazzottius varieornatus (invertebrata)
Gene: RvY_15762-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D1VW28
#2: Chemical ChemComp-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: Protein bound to mevalonate at about 3 mg/mL was set up in 150 nL plus 150 nL drops over 50 microlitres of reservoir which contained: 0.126 M calcium acetate, 24.9 v/v PEG 400, 0.09 M sodium ...Details: Protein bound to mevalonate at about 3 mg/mL was set up in 150 nL plus 150 nL drops over 50 microlitres of reservoir which contained: 0.126 M calcium acetate, 24.9 v/v PEG 400, 0.09 M sodium HEPES pH 8.4 with 10 mM taurine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953723 Å / Relative weight: 1
ReflectionResolution: 2→45.1 Å / Num. obs: 52511 / % possible obs: 99.8 % / Redundancy: 27.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.057 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 26.8 % / Rmerge(I) obs: 4.656 / Mean I/σ(I) obs: 1 / Num. unique obs: 3787 / CC1/2: 0.623 / Rpim(I) all: 0.9 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.091 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.174 / SU B: 7.226 / SU ML: 0.181 / Average fsc free: 0.9403 / Average fsc work: 0.9525 / Cross valid method: FREE R-VALUE / ESU R: 0.208 / ESU R Free: 0.176
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2471 2598 4.968 %
Rwork0.2079 49698 -
all0.21 --
obs-52296 99.979 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.413 Å2
Baniso -1Baniso -2Baniso -3
1-2.539 Å2-0 Å2-0 Å2
2--1.818 Å2-0 Å2
3----4.357 Å2
Refinement stepCycle: LAST / Resolution: 2→44.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 35 151 6071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126038
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165893
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.6468172
X-RAY DIFFRACTIONr_angle_other_deg0.4311.57513576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.415538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.159101063
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.35310234
X-RAY DIFFRACTIONr_chiral_restr0.0580.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021263
X-RAY DIFFRACTIONr_nbd_refined0.2060.21242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.25327
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22984
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23271
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2179
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.224
X-RAY DIFFRACTIONr_nbd_other0.2130.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0730.21
X-RAY DIFFRACTIONr_mcbond_it3.1084.1333119
X-RAY DIFFRACTIONr_mcbond_other3.1084.1333119
X-RAY DIFFRACTIONr_mcangle_it4.7127.4153897
X-RAY DIFFRACTIONr_mcangle_other4.7127.4173898
X-RAY DIFFRACTIONr_scbond_it3.7814.5362919
X-RAY DIFFRACTIONr_scbond_other3.784.5362920
X-RAY DIFFRACTIONr_scangle_it5.8978.1634275
X-RAY DIFFRACTIONr_scangle_other5.8968.1634276
X-RAY DIFFRACTIONr_lrange_it8.84249.89425678
X-RAY DIFFRACTIONr_lrange_other8.84749.88625625
X-RAY DIFFRACTIONr_ncsr_local_group_10.1160.0511684
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.115820.05008
12AX-RAY DIFFRACTIONLocal ncs0.115820.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3481810.35436510.35438330.8690.8899.97390.327
2.052-2.1080.3461920.33334570.33336500.8930.89199.97260.304
2.108-2.1690.3231710.29834460.29936170.9060.9131000.263
2.169-2.2350.2971930.27333190.27435130.9290.93899.97150.236
2.235-2.3090.2961780.25232200.25433980.9240.9451000.215
2.309-2.3890.2771420.23231650.23433070.9320.9581000.194
2.389-2.4790.2521630.20830040.21131670.9610.9681000.173
2.479-2.580.2631350.21529330.21730680.9490.9681000.182
2.58-2.6950.2681470.22328060.22529530.9530.9691000.19
2.695-2.8260.2491350.2127000.21228350.9640.9731000.176
2.826-2.9780.2761360.20425530.20726890.9490.9741000.171
2.978-3.1570.2511170.20824310.2125480.9590.9721000.182
3.157-3.3740.2661220.19722900.224120.9590.9751000.173
3.374-3.6430.2411220.19121330.19422560.9630.97899.95570.171
3.643-3.9880.176980.16919920.16920910.9790.98399.95220.151
3.988-4.4540.2061050.15918010.16219060.9750.9851000.144
4.454-5.1340.211810.16316140.16616950.9770.9861000.146
5.134-6.2670.259740.20313840.20614580.970.9811000.18
6.267-8.7740.226730.16910900.17211630.9710.9841000.154
8.774-44.0910.179320.2076890.2067210.9860.9821000.204

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