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- PDB-3wyi: Structure of S. aureus undecaprenyl diphosphate synthase -

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Basic information

Entry
Database: PDB / ID: 3wyi
TitleStructure of S. aureus undecaprenyl diphosphate synthase
ComponentsIsoprenyl transferase
KeywordsTRANSFERASE / isopentenyl diphosphate binding / product inhibition
Function / homologyUndecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGao, J. / Ko, T.P. / Huang, C.H. / Oldfield, E. / Guo, R.T.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Antibacterial drug leads: DNA and enzyme multitargeting.
Authors: Zhu, W. / Wang, Y. / Li, K. / Gao, J. / Huang, C.H. / Chen, C.C. / Ko, T.P. / Zhang, Y. / Guo, R.T. / Oldfield, E.
History
DepositionAug 29, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9513
Polymers29,9021
Non-polymers492
Water6,756375
1
A: Isoprenyl transferase
hetero molecules

A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9026
Polymers59,8042
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4070 Å2
ΔGint-48 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.080, 62.080, 133.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Isoprenyl transferase


Mass: 29902.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: CH52_12785 / Plasmid: pET46Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: W8UYA6, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM HEPES, pH 6.5, 200mM Magnesium chloride, 200mM Nickel chloride, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 20923 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 32.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.6 / Num. unique all: 17400 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H8E

4h8e


Resolution: 2→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.227 -random
Rwork0.19 --
all-20083 -
obs-19109 -
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 2 375 2270
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.301 1731
Rwork0.267 -
obs-20083

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