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

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Basic information

Entry
Database: PDB / ID: 4dpy
TitleCrystal structure of Staphylococcus epidermidis S192A 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: 2.14 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)74,3754
Polymers73,7092
Non-polymers6662
Water7,188399
1
A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1882
Polymers36,8541
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1882
Polymers36,8541
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.678, 101.733, 155.498
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-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.: 399 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
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: 2.14→50 Å / Num. all: 32959 / Num. obs: 31316 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.7
Reflection shellResolution: 2.14→2.2027 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.29 / % possible all: 75

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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: 2.14→48.346 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8524 / SU ML: 0.28 / σ(F): 0 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1643 4.98 %RANDOM
Rwork0.1678 ---
all0.1707 32959 --
obs0.1707 31316 90.21 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.741 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 92.13 Å2 / Biso mean: 26.7167 Å2 / Biso min: 5.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.9438 Å20 Å2-0 Å2
2--2.4879 Å2-0 Å2
3----1.5442 Å2
Refinement stepCycle: LAST / Resolution: 2.14→48.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 0 40 399 5522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085226
X-RAY DIFFRACTIONf_angle_d1.0177073
X-RAY DIFFRACTIONf_chiral_restr0.067784
X-RAY DIFFRACTIONf_plane_restr0.004919
X-RAY DIFFRACTIONf_dihedral_angle_d13.1351935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.20270.29761100.20022122223275
2.2027-2.27380.29461220.20992317243981
2.2738-2.35510.27961240.1992376250083
2.3551-2.44940.25421290.18852452258186
2.4494-2.56090.24861340.18572561269590
2.5609-2.69590.25451370.19282589272690
2.6959-2.86480.24991410.17862696283793
2.8648-3.08590.24711440.17672735287995
3.0859-3.39640.23271450.17322769291496
3.3964-3.88770.221490.15892813296297
3.8877-4.89730.17241510.12712864301598
4.8973-48.35790.18161570.15823022317999

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