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- PDB-2hfs: Crystal structure of L. major mevalonate kinase -

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Basic information

Entry
Database: PDB / ID: 2hfs
TitleCrystal structure of L. major mevalonate kinase
ComponentsMevalonate kinase, putative
KeywordsTRANSFERASE / GHMP kinase / mevalonate kinase / Trypanosomatid parasite
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / glycosome / ATP binding / cytosol
Similarity search - Function
Mevalonate kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup ...Mevalonate kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsSgraja, T. / Hunter, W.N.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Structure, substrate recognition and reactivity of Leishmania major mevalonate kinase.
Authors: Sgraja, T. / Smith, T.K. / Hunter, W.N.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mevalonate kinase, putative
B: Mevalonate kinase, putative


Theoretical massNumber of molelcules
Total (without water)71,9992
Polymers71,9992
Non-polymers00
Water10,629590
1
A: Mevalonate kinase, putative


Theoretical massNumber of molelcules
Total (without water)35,9991
Polymers35,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate kinase, putative


Theoretical massNumber of molelcules
Total (without water)35,9991
Polymers35,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.265, 88.466, 88.167
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit.

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Components

#1: Protein Mevalonate kinase, putative


Mass: 35999.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q4Q6K7, mevalonate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.2M sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97945
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2005
RadiationMonochromator: Khuzo monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 61265 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.056 / Rsym value: 0.05 / Net I/σ(I): 20.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.42 / % possible all: 92.6

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.72 / FOM acentric: 0.72 / FOM centric: 0.69 / Reflection: 41108 / Reflection acentric: 39877 / Reflection centric: 1231
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-36.5260.880.890.7718231658165
3.6-5.70.920.930.8555595305254
2.9-3.60.870.880.8469576735222
2.5-2.90.750.760.6269616771190
2.1-2.50.640.640.541230912040269
2-2.10.490.490.4274997368131

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.75→33.43 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.87 / SU B: 3.537 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27652 3109 5.1 %RANDOM
Rwork0.21652 ---
obs0.21958 57584 100 %-
all-60693 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.219 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 0 590 5616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225120
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9496935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7075670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77624.364220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09815885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.291532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.22608
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23553
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2472
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.33633365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68135252
X-RAY DIFFRACTIONr_scbond_it2.58651958
X-RAY DIFFRACTIONr_scangle_it3.28851683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 205 -
Rwork0.277 4164 -
obs--100 %

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