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- PDB-4dpx: Crystal structure of S192A Staphylococcus epidermidis mevalonate ... -

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Basic information

Entry
Database: PDB / ID: 4dpx
TitleCrystal structure of S192A 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
FORMIC ACID / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsBarta, M.L. / McWhorter, W.J. / Geisbrecht, B.V.
CitationJournal: Biochemistry / Year: 2012
Title: Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Authors: Barta, M.L. / McWhorter, W.J. / Miziorko, H.M. / Geisbrecht, B.V.
History
DepositionFeb 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 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)74,21510
Polymers73,7092
Non-polymers5068
Water9,980554
1
A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1315
Polymers36,8541
Non-polymers2764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0855
Polymers36,8541
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.922, 102.273, 155.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mevalonate diphosphate 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 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9FD73, diphosphomevalonate decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
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: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2011 / Details: mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. all: 48025 / Num. obs: 46055 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 20.69 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.3
Reflection shellResolution: 1.948→1.9972 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 5.83 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QT5

3qt5


Resolution: 1.948→48.591 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8836 / SU ML: 0.24 / σ(F): 0 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 1970 4.1 %RANDOM
Rwork0.1624 ---
all0.164 48025 --
obs0.164 46055 98.56 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.03 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 100 Å2 / Biso mean: 23.963 Å2 / Biso min: 7.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--1.5863 Å20 Å2
3----1.9663 Å2
Refinement stepCycle: LAST / Resolution: 1.948→48.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 33 554 5681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075219
X-RAY DIFFRACTIONf_angle_d1.0057040
X-RAY DIFFRACTIONf_chiral_restr0.067782
X-RAY DIFFRACTIONf_plane_restr0.004915
X-RAY DIFFRACTIONf_dihedral_angle_d13.0981920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.948-1.99720.25161290.18263099322894
1.9972-2.05120.21911340.16583185331997
2.0512-2.11150.23171360.17463212334897
2.1115-2.17970.2291390.17753232337198
2.1797-2.25760.23571410.16933240338198
2.2576-2.3480.19341410.16793269341098
2.348-2.45480.24251410.16153283342499
2.4548-2.58420.2131400.16673274341499
2.5842-2.74610.22661430.16933413484100
2.7461-2.95820.19321430.171733153458100
2.9582-3.25580.21891430.167233423485100
3.2558-3.72680.18681440.163933583502100
3.7268-4.69470.15471460.135534013547100
4.6947-48.60580.18241500.160635043654100

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