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

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Basic information

Entry
Database: PDB / ID: 4dpu
TitleCrystal structure of Staphylococcus epidermidis S192A mevalonate diphosphate decarboxylase complexed with inhibitor 6-FMVAPP and ATPgS
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Chem-FM0 / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: Mevalonate diphosphate decarboxylase
B: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4076
Polymers73,7092
Non-polymers1,6994
Water8,791488
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A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7043
Polymers36,8541
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7043
Polymers36,8541
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.732, 103.140, 156.749
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-FM0 / (3R)-3-(fluoromethyl)-3-hydroxy-5-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}pentanoic acid / 6-fluoromevalonate 5-diphosphate


Mass: 326.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13FO10P2
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
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: Apr 1, 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: 1.9→50 Å / Num. all: 51535 / Num. obs: 49578 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Biso Wilson estimate: 26.01 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.5
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.2 / % possible all: 86

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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: 1.9→49.82 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8509 / SU ML: 0.24 / σ(F): 0 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1957 3.8 %RANDOM
Rwork0.1791 ---
all0.1808 51535 --
obs0.1808 49578 97.08 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.649 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 93.26 Å2 / Biso mean: 28.2014 Å2 / Biso min: 13.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.1224 Å20 Å2-0 Å2
2--1.6154 Å2-0 Å2
3----1.7378 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5125 0 100 488 5713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075315
X-RAY DIFFRACTIONf_angle_d1.0587199
X-RAY DIFFRACTIONf_chiral_restr0.067792
X-RAY DIFFRACTIONf_plane_restr0.004922
X-RAY DIFFRACTIONf_dihedral_angle_d17.3931979
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 (%)
1.9-1.94780.30781290.24723151328086
1.9478-2.00040.29531320.22393342347493
2.0004-2.05930.28421340.20583408354295
2.0593-2.12570.24231390.20083467360696
2.1257-2.20170.23611400.19233508364897
2.2017-2.28990.27661370.20233525366297
2.2899-2.39410.25171390.19843535367498
2.3941-2.52030.25871400.19693562370298
2.5203-2.67820.2541420.19513600374299
2.6782-2.8850.20041430.18693643378699
2.885-3.17530.23591410.184936363777100
3.1753-3.63460.22971440.174336583802100
3.6346-4.57870.16611470.14637113858100
4.5787-49.83660.19941500.158938323982100

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