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- PDB-3qt8: Crystal structure of mutant S192A Staphylococcus epidermidis meva... -

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Basic information

Entry
Database: PDB / ID: 3qt8
TitleCrystal structure of mutant S192A Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP
ComponentsMevalonate diphosphate decarboxylase
KeywordsLYASE/LYASE INHIBITOR / GHMP kinase family / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / ATP binding / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-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
Chem-FM0 / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBarta, M.L. / Skaff, A.D. / McWhorter, W.J. / Miziorko, H.M. / Geisbrecht, B.V.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structures of Staphylococcus epidermidis mevalonate diphosphate decarboxylase bound to inhibitory analogs reveal new insight into substrate binding and catalysis.
Authors: Barta, M.L. / Skaff, D.A. / McWhorter, W.J. / Herdendorf, T.J. / Miziorko, H.M. / Geisbrecht, B.V.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 diphosphate decarboxylase
B: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4535
Polymers73,7092
Non-polymers7443
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-16 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.505, 101.367, 155.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mevalonate diphosphate decarboxylase / Diphosphomevalonate decarboxylase


Mass: 36854.395 Da / Num. of mol.: 2 / Mutation: S192A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: mvaD / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FD73, diphosphomevalonate decarboxylase
#2: Chemical ChemComp-FM0 / (3R)-3-(fluoromethyl)-3-hydroxy-5-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}pentanoic acid / 6-fluoromevalonate 5-diphosphate


Mass: 326.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13FO10P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.25 M sodium formate, 16% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2011
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.376 Å / Num. all: 34009 / Num. obs: 34008 / % possible obs: 86.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3314 / % possible all: 87.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QT5

3qt5


Resolution: 2.1→29.004 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 1665 5 %RANDOM
Rwork0.1903 ---
all0.1928 ---
obs0.1928 33267 86.84 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.225 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.884 Å20 Å20 Å2
2--6.5508 Å20 Å2
3----1.6228 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5065 0 44 278 5387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085192
X-RAY DIFFRACTIONf_angle_d1.0877014
X-RAY DIFFRACTIONf_dihedral_angle_d14.841940
X-RAY DIFFRACTIONf_chiral_restr0.067776
X-RAY DIFFRACTIONf_plane_restr0.004906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.1750.33371560.27242885X-RAY DIFFRACTION80
2.175-2.2620.29461600.23833006X-RAY DIFFRACTION84
2.262-2.36490.2811620.23643033X-RAY DIFFRACTION84
2.3649-2.48950.32351630.2213102X-RAY DIFFRACTION86
2.4895-2.64540.24691590.21553115X-RAY DIFFRACTION86
2.6454-2.84950.30081670.21413133X-RAY DIFFRACTION86
2.8495-3.13590.24271610.20923109X-RAY DIFFRACTION86
3.1359-3.5890.23721680.19313173X-RAY DIFFRACTION87
3.589-4.5190.21711690.15073256X-RAY DIFFRACTION89
4.519-29.00660.18282000.15783790X-RAY DIFFRACTION99

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