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- PDB-3qt6: Crystal structure of Staphylococcus epidermidis mevalonate diphos... -

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Basic information

Entry
Database: PDB / ID: 3qt6
TitleCrystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with inhibitor DPGP
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-2P0 / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.047 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)74,4074
Polymers73,7412
Non-polymers6662
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-18 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.670, 101.442, 154.639
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: Chemical ChemComp-2P0 / 1-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-L-proline / diphosphoglycolylproline


Type: L-peptide linking / Mass: 333.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 44.05 %
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: 2.047→49.34 Å / Num. all: 41214 / Num. obs: 41213 / % possible obs: 98.22 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 13.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 26.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 5.1 / Num. unique all: 4081 / % possible all: 100

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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: 2.047→29.601 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 1967 4.85 %RANDOM
Rwork0.183 ---
all0.1851 ---
obs0.1851 40540 98.22 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.897 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.953 Å20 Å2-0 Å2
2--3.6269 Å2-0 Å2
3----3.4521 Å2
Refinement stepCycle: LAST / Resolution: 2.047→29.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 40 312 5430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075205
X-RAY DIFFRACTIONf_angle_d1.0347035
X-RAY DIFFRACTIONf_dihedral_angle_d13.8281955
X-RAY DIFFRACTIONf_chiral_restr0.067776
X-RAY DIFFRACTIONf_plane_restr0.004913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0469-2.120.26851850.2243619X-RAY DIFFRACTION93
2.12-2.20490.27141940.21763709X-RAY DIFFRACTION96
2.2049-2.30520.26781960.21523800X-RAY DIFFRACTION97
2.3052-2.42660.25581960.21093834X-RAY DIFFRACTION98
2.4266-2.57860.27891920.2043831X-RAY DIFFRACTION99
2.5786-2.77760.23991970.20443864X-RAY DIFFRACTION99
2.7776-3.05680.26931960.19693900X-RAY DIFFRACTION99
3.0568-3.49850.2482010.18183940X-RAY DIFFRACTION100
3.4985-4.40550.17862020.15223985X-RAY DIFFRACTION100
4.4055-29.60420.18492080.16324091X-RAY DIFFRACTION100

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