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- PDB-5v2m: Mevalonate diphosphate mediated ATP binding mechanism of the meva... -

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Basic information

Entry
Database: PDB / ID: 5v2m
TitleMevalonate diphosphate mediated ATP binding mechanism of the mevalonate diphosphate decarboxylase from Enterococcus faecalis
ComponentsMevalonate diphosphate decarboxylase
KeywordsLYASE / The mevalonate pathway / Vancomycin resistant enterococci / Enzyme kinetics / isothermal titration calorimetry.
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / metal ion 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 speciesEnterococcus faecalis V583 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.989 Å
AuthorsStauffacher, C.V. / Chen, C.-L.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Mevalonate 5-diphosphate mediates ATP binding to the mevalonate diphosphate decarboxylase from the bacterial pathogen Enterococcus faecalis.
Authors: Chen, C.L. / Mermoud, J.C. / Paul, L.N. / Steussy, C.N. / Stauffacher, C.V.
History
DepositionMar 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7992
Polymers36,7031
Non-polymers961
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.934, 98.078, 46.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Mevalonate diphosphate decarboxylase


Mass: 36702.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis V583 (bacteria) / Gene: mvaD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FD68, UniProt: Q837E0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.6 M ammonium sulfate, 50 mM sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 26117 / % possible obs: 95.4 % / Redundancy: 5.9 % / Rpim(I) all: 0.027 / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.07 Å / CC1/2: 0.991 / Rpim(I) all: 0.058

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2L

5v2l


Resolution: 1.989→19.673 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1257 5.13 %Random selection
Rwork0.1795 ---
obs0.1807 24481 93.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.989→19.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 5 150 2571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122691
X-RAY DIFFRACTIONf_angle_d1.1013643
X-RAY DIFFRACTIONf_dihedral_angle_d15.966977
X-RAY DIFFRACTIONf_chiral_restr0.06401
X-RAY DIFFRACTIONf_plane_restr0.008469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9889-2.06840.23031190.19752137X-RAY DIFFRACTION79
2.0684-2.16250.19881520.17292417X-RAY DIFFRACTION90
2.1625-2.27630.16321280.16832557X-RAY DIFFRACTION94
2.2763-2.41870.23021480.16182669X-RAY DIFFRACTION97
2.4187-2.60510.23791360.1732670X-RAY DIFFRACTION98
2.6051-2.86650.19511490.17472727X-RAY DIFFRACTION99
2.8665-3.27960.22141500.18712754X-RAY DIFFRACTION99
3.2796-4.12570.17711430.16962681X-RAY DIFFRACTION96
4.1257-19.67410.20781320.19772612X-RAY DIFFRACTION89

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