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- PDB-3qt5: Crystal structure of Staphylococcus epidermidis mevalonate diphos... -

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Basic information

Entry
Database: PDB / ID: 3qt5
TitleCrystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase
ComponentsMevalonate diphosphate decarboxylase
KeywordsLYASE / GHMP kinase family
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
diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)73,7412
Polymers73,7412
Non-polymers00
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.983, 101.987, 155.771
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: 36870.395 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
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: 1.848→49.616 Å / Num. all: 52599 / Num. obs: 52598 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2.47 / Num. unique all: 4552 / % possible all: 81.5

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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 2HK2

2hk2


Resolution: 1.848→26.905 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1945 3.8 %RANDOM
Rwork0.1949 ---
all0.1961 51149 --
obs0.1961 51149 90.06 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.18 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6064 Å20 Å2-0 Å2
2--0.2848 Å2-0 Å2
3----1.4451 Å2
Refinement stepCycle: LAST / Resolution: 1.848→26.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 0 388 5466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075164
X-RAY DIFFRACTIONf_angle_d0.9916971
X-RAY DIFFRACTIONf_dihedral_angle_d12.7881903
X-RAY DIFFRACTIONf_chiral_restr0.067773
X-RAY DIFFRACTIONf_plane_restr0.004908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8481-1.91410.29981460.27053812X-RAY DIFFRACTION71
1.9141-1.99070.2961660.24714226X-RAY DIFFRACTION78
1.9907-2.08130.27861790.23464492X-RAY DIFFRACTION83
2.0813-2.1910.28611880.22394694X-RAY DIFFRACTION86
2.191-2.32810.30041930.22174879X-RAY DIFFRACTION90
2.3281-2.50780.24592050.21655165X-RAY DIFFRACTION95
2.5078-2.75990.25162100.21465317X-RAY DIFFRACTION98
2.7599-3.15880.24112150.20425422X-RAY DIFFRACTION99
3.1588-3.97760.19062180.17215512X-RAY DIFFRACTION100
3.9776-26.90830.17812250.15975685X-RAY DIFFRACTION100

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