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- PDB-4du7: Crystal structure of Staphylococcus epidermidis mevalonate diphos... -

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Basic information

Entry
Database: PDB / ID: 4du7
TitleCrystal structure of Staphylococcus epidermidis mevalonate diphosphate decarboxylase complexed with substrate mevalonate diphosphate
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
Chem-DP6 / FORMIC ACID / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 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 21, 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)74,4035
Polymers73,7412
Non-polymers6623
Water4,900272
1
A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1792
Polymers36,8701
Non-polymers3081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2253
Polymers36,8701
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.592, 101.320, 154.932
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: 36870.395 Da / Num. of mol.: 2
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-DP6 / (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID


Mass: 308.117 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O10P2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 44.03 %
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: 23-BM-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2011 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 31892 / Num. obs: 30297 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 30.71 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 19.8
Reflection shellResolution: 2.2→2.2716 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.04 / % possible all: 88

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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: 2.201→31.261 Å / Occupancy max: 1 / Occupancy min: 0.69 / FOM work R set: 0.8095 / SU ML: 0.28 / σ(F): 0 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1595 5 %RANDOM
Rwork0.1915 ---
all0.1939 31892 --
obs0.1939 30297 95.68 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.724 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 99.52 Å2 / Biso mean: 34.9367 Å2 / Biso min: 17.52 Å2
Baniso -1Baniso -2Baniso -3
1--5.1735 Å20 Å2-0 Å2
2--6.5302 Å2-0 Å2
3----1.5421 Å2
Refinement stepCycle: LAST / Resolution: 2.201→31.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 39 272 5366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075177
X-RAY DIFFRACTIONf_angle_d0.9716995
X-RAY DIFFRACTIONf_chiral_restr0.065774
X-RAY DIFFRACTIONf_plane_restr0.004905
X-RAY DIFFRACTIONf_dihedral_angle_d14.7251916
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.201-2.27160.34591350.27212499263488
2.2716-2.35270.33791380.25672580271891
2.3527-2.44690.30091320.24192645277793
2.4469-2.55820.27381410.22812682282394
2.5582-2.6930.31471440.22312733287796
2.693-2.86160.27611480.21472765291397
2.8616-3.08240.25951480.20822793294197
3.0824-3.39230.2631490.20152832298199
3.3923-3.88230.21371500.17332887303799
3.8823-4.88830.18111530.14729123065100
4.8883-31.26380.1911570.16612969312698

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