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- PDB-3wyj: Structure of E. coli undecaprenyl diphosphate synthase in complex... -

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Basic information

Entry
Database: PDB / ID: 3wyj
TitleStructure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789
ComponentsDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
KeywordsTRANSFERASE
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / manganese ion binding ...Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / manganese ion binding / regulation of cell shape / cell cycle / cell division / magnesium ion binding / protein homodimerization activity / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H78 / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Aug 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 1.2Nov 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: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
B: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9113
Polymers56,9622
Non-polymers9491
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-13 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.712, 68.995, 108.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) / Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / ...Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / Undecaprenyl pyrophosphate synthase / UPP synthase


Mass: 28481.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b0174, ispU, JW0169, rth, uppS, yaeS / Plasmid: pET32Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-H78 / [1-oxidanyl-2-[3-[3-[[3-[[3-[3-(2-oxidanyl-2,2-diphosphono-ethyl)phenyl]phenyl]sulfamoyl]phenyl]sulfonylamino]phenyl]phenyl]-1-phosphono-ethyl]phosphonic acid


Mass: 948.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36N2O18P4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% Ethylene glycol, 2-5% PEG 35K, pH 7.5, 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: Feb 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 28793 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 39.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 6 / Num. unique all: 16257 / % possible all: 99.7

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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: 2.0E+98 / Resolution: 2.1→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 -random
Rwork0.2 --
all-28076 -
obs-26715 -
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 60 425 3988
LS refinement shellResolution: 2→2.18 Å
RfactorNum. reflection
Rfree0.3 2526
Rwork0.228 -
obs-28076

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