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- PDB-2hk2: Crystal structure of mevalonate diphosphate decarboxylase from St... -

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Basic information

Entry
Database: PDB / ID: 2hk2
TitleCrystal structure of mevalonate diphosphate decarboxylase from Staphylococcus aureus (monoclinic form)
ComponentsDiphosphomevalonate decarboxylase
KeywordsLYASE / mevalonate diphosphate decarboxylase / diphosphomevalonate decarboxylase / decarboxylase
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / 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 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / 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
Diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsByres, E. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of Trypanosoma brucei and Staphylococcus aureus Mevalonate Diphosphate Decarboxylase Inform on the Determinants of Specificity and Reactivity
Authors: Byres, E. / Alphey, M.S. / Smith, T.K. / Hunter, W.N.
History
DepositionJul 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphosphomevalonate decarboxylase
B: Diphosphomevalonate decarboxylase


Theoretical massNumber of molelcules
Total (without water)74,7502
Polymers74,7502
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-19 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.495, 53.061, 100.882
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 1 - 326 / Label seq-ID: 5 - 330

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a dimer. There is one biological unit in the asymmetric unit (chains A & B)

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Components

#1: Protein Diphosphomevalonate decarboxylase / Mevalonate diphosphate decarboxylase


Mass: 37375.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mvaD / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2FJ52, UniProt: Q9FD84*PLUS, diphosphomevalonate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 1.8M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionRedundancy: 5.2 % / Av σ(I) over netI: 6.6 / Number: 208737 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / D res high: 2.3 Å / D res low: 100.526 Å / Num. obs: 40530 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.2746.9399.710.0630.0634.6
5.147.2710010.0550.0555.1
4.25.1410010.0540.0545.1
3.644.210010.0570.0575.2
3.253.6410010.0720.0725.2
2.973.2510010.0950.0955.2
2.752.9710010.1330.1335.2
2.572.7510010.180.185.2
2.422.5710010.2390.2395.2
2.32.4210010.2950.2955.1
ReflectionResolution: 2.3→46.92 Å / Num. all: 40530 / Num. obs: 40530 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.5 / Num. measured all: 30232 / Num. unique all: 5875 / Rsym value: 0.295 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→46.92 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 6.15 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2030 5 %RANDOM
Rwork0.191 ---
all0.194 40530 --
obs0.191 40530 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å2-0.24 Å2
2---0.82 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5255 0 0 406 5661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225359
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9497241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.87425.116258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.82415961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.9151524
X-RAY DIFFRACTIONr_chiral_restr0.1330.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024040
X-RAY DIFFRACTIONr_nbd_refined0.2190.22547
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2449
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.222
X-RAY DIFFRACTIONr_mcbond_it0.9151.53390
X-RAY DIFFRACTIONr_mcangle_it1.51625288
X-RAY DIFFRACTIONr_scbond_it2.42332268
X-RAY DIFFRACTIONr_scangle_it3.854.51953
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2574 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.215
LOOSE THERMAL1.9510
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 130 -
Rwork0.215 2834 -
obs-2964 100 %

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