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- PDB-8teb: Structure of MKbur -

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Basic information

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


mevalonate kinase / mevalonate kinase activity / galactokinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / galactose metabolic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Mevalonate kinase, archaeal / Mevalonate kinase / Galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / 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 ...Mevalonate kinase, archaeal / Mevalonate kinase / Galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / 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
Biological speciesMethanococcoides burtonii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,2946
Polymers66,1372
Non-polymers1574
Water3,639202
1
A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1904
Polymers33,0681
Non-polymers1223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1042
Polymers33,0681
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.338, 93.034, 90.389
Angle α, β, γ (deg.)90.000, 90.045, 90.000
Int Tables number4
Space group name H-MP1211
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: GLN / End label comp-ID: GLN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 303 / Label seq-ID: 1 - 303

Dom-ID
1
2

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

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Components

#1: Protein Mevalonate kinase


Mass: 33068.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcoides burtonii (archaea) / Gene: mvk / Production host: Escherichia coli (E. coli) / References: UniProt: Q12TI0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Sitting drops were set up with 150 nL plus 150 nL volumes over 50 microlitre wells; the crystallisation reservoir contained: 20% PEG 8000, 200 mM MgCl2, 100 mM tris pH 8.5 and 3% trehalose. ...Details: Sitting drops were set up with 150 nL plus 150 nL volumes over 50 microlitre wells; the crystallisation reservoir contained: 20% PEG 8000, 200 mM MgCl2, 100 mM tris pH 8.5 and 3% trehalose. The protein concentration was about 24 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→46.5 Å / Num. obs: 32249 / % possible obs: 99.5 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.046 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2760 / CC1/2: 0.849 / Rpim(I) all: 0.285 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.335 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2382 1503 4.664 %
Rwork0.1857 30725 -
all0.188 --
obs-32228 99.368 %
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: 34.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.669 Å2-0 Å2-0.862 Å2
2--0.992 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 7 202 4616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124465
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164317
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.636067
X-RAY DIFFRACTIONr_angle_other_deg0.4371.569964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.826520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88810738
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.96510158
X-RAY DIFFRACTIONr_chiral_restr0.060.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined0.2090.2890
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24017
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22294
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2207
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.25
X-RAY DIFFRACTIONr_nbd_other0.1370.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0250.21
X-RAY DIFFRACTIONr_mcbond_it2.943.3682440
X-RAY DIFFRACTIONr_mcbond_other2.9393.3692440
X-RAY DIFFRACTIONr_mcangle_it4.3586.0443047
X-RAY DIFFRACTIONr_mcangle_other4.3586.0453048
X-RAY DIFFRACTIONr_scbond_it3.9423.8412025
X-RAY DIFFRACTIONr_scbond_other3.9413.8422026
X-RAY DIFFRACTIONr_scangle_it6.096.93019
X-RAY DIFFRACTIONr_scangle_other6.0896.93020
X-RAY DIFFRACTIONr_lrange_it8.51240.45719349
X-RAY DIFFRACTIONr_lrange_other8.51240.47619249
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.059256
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.088110.05009
12AX-RAY DIFFRACTIONLocal ncs0.088110.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2540.2791340.252251X-RAY DIFFRACTION97.4663
2.254-2.3160.2881080.2262165X-RAY DIFFRACTION99.4313
2.316-2.3830.299810.2072187X-RAY DIFFRACTION99.3865
2.383-2.4560.256980.2032058X-RAY DIFFRACTION99.172
2.456-2.5360.2921010.2032009X-RAY DIFFRACTION99.7164
2.536-2.6250.255930.2061948X-RAY DIFFRACTION99.7069
2.625-2.7240.2461030.1921902X-RAY DIFFRACTION99.7016
2.724-2.8340.2291090.1981769X-RAY DIFFRACTION99.523
2.834-2.960.246950.1861772X-RAY DIFFRACTION99.6265
2.96-3.1040.243730.1931630X-RAY DIFFRACTION98.4393
3.104-3.2710.283860.1981570X-RAY DIFFRACTION99.8192
3.271-3.4680.272490.1981555X-RAY DIFFRACTION99.9377
3.468-3.7060.199680.1911410X-RAY DIFFRACTION99.8649
3.706-4.0010.181470.1721327X-RAY DIFFRACTION100
4.001-4.380.213770.1481217X-RAY DIFFRACTION100
4.38-4.8910.18700.1371095X-RAY DIFFRACTION99.6578
4.891-5.6370.226310.167995X-RAY DIFFRACTION99.4186
5.637-6.8790.253330.194818X-RAY DIFFRACTION98.1546
6.879-9.6240.256340.145656X-RAY DIFFRACTION100
9.624-46.50.239130.204391X-RAY DIFFRACTION100

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