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- PDB-2x7i: Crystal structure of mevalonate kinase from methicillin-resistant... -

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Basic information

Entry
Database: PDB / ID: 2x7i
TitleCrystal structure of mevalonate kinase from methicillin-resistant Staphylococcus aureus MRSA252
ComponentsMEVALONATE KINASE
KeywordsTRANSFERASE / KINASE
Function / homologyGHMP kinase, C-terminal domain / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / CITRIC ACID / Mevalonate kinase / Mevalonate kinase
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsOke, M. / Yan, X. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: MEVALONATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3443
Polymers33,1161
Non-polymers2282
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.589, 94.589, 169.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

21A-2051-

HOH

31A-2101-

HOH

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Components

#1: Protein MEVALONATE KINASE /


Mass: 33115.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MRSA252 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GJ78, UniProt: A0A7U7EU40*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.3 Å3/Da / Density % sol: 62.3 % / Description: NONE
Crystal growpH: 4
Details: 0.1 M CITRIC ACID PH 4.0, 3.6 M SODIUM CHLORIDE. THE CRYSTALS WERE CRYOPROTECTED BY ADDING 25% PEG400 INTO THE SCREEN SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 27, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 2.2→81.92 Å / Num. obs: 17784 / % possible obs: 80.3 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 50.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.2→81.92 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.053 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ORDERED FROM RESIDUE 2-306. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 967 5.2 %RANDOM
Rwork0.21105 ---
obs0.21335 17784 80.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.542 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å21.67 Å2-0 Å2
2--3.33 Å2-0 Å2
3----5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→81.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 14 126 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222288
X-RAY DIFFRACTIONr_bond_other_d0.0010.021522
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9653093
X-RAY DIFFRACTIONr_angle_other_deg0.81133755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18324.94387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93515402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.875157
X-RAY DIFFRACTIONr_chiral_restr0.0620.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3851.51457
X-RAY DIFFRACTIONr_mcbond_other0.0691.5608
X-RAY DIFFRACTIONr_mcangle_it0.74222332
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1593831
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.964.5760
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 52 -
Rwork0.34 781 -
obs--50.18 %
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)
13.57140.30870.78390.59910.20481.20140.0414-0.1057-0.29470.04630.0837-0.18390.29890.1331-0.12520.21020.0501-0.03210.0452-0.00070.1157-23.95519.84528.112
25.1397-2.33182.84992.8209-1.70045.7969-0.093-0.4483-0.22070.42890.04910.0057-0.0554-0.05220.04390.1724-0.0026-0.03610.06470.03410.0593-27.73716.55534.749
397.54640.0004-0.013436.4355-0.01580.5474-0.4386-1.83226.4425-0.67340.86390.22590.2791-0.3676-0.42530.2672-0.1455-0.15420.3450.10860.6595-29.5527.15321.131
42.85790.17630.96871.11320.66513.68670.034-0.2153-0.03260.0181-0.02610.13530.2718-0.1891-0.00790.12460.0108-0.04290.04820.02990.0867-39.16320.69125.192
50.4018-2.66431.033719.3385-7.4842.92770.10250.34610.9069-0.826-2.0922-4.98210.28320.6931.98980.59380.03420.17360.85140.70282.7636-32.37635.8089.858
61.7442-1.5554-0.15344.62550.41996.72990.11070.22620.0446-0.34630.0047-0.0059-0.17810.2131-0.11530.1907-0.0129-0.11740.10830.00040.0942-43.8124.0234.995
72.3198-0.29530.63313.60791.04663.54510.14410.379-0.3743-0.34090.0116-0.31030.36840.2618-0.15570.25210.025-0.04870.1362-0.06070.1263-33.09215.5885.52
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 98
2X-RAY DIFFRACTION2A99 - 120
3X-RAY DIFFRACTION3A1307
4X-RAY DIFFRACTION4A121 - 183
5X-RAY DIFFRACTION5A184 - 203
6X-RAY DIFFRACTION6A204 - 257
7X-RAY DIFFRACTION7A258 - 306

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