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- PDB-2e9d: E. coli undecaprenyl pyrophosphate synthase in complex with BPH-676 -

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Basic information

Entry
Database: PDB / ID: 2e9d
TitleE. coli undecaprenyl pyrophosphate synthase in complex with BPH-676
ComponentsUndecaprenyl pyrophosphate synthetase
KeywordsTRANSFERASE / cell wall / prenyltransferase / farnesyl pyrophosphate / bisphosphonate / antibiotic
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding ...Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-B76 / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGuo, R.T. / Cao, R. / Ko, T.P. / Liang, P.H. / Oldfield, E. / Wang, A.H.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases
Authors: Guo, R.T. / Cao, R. / Liang, P.H. / Ko, T.P. / Chang, T.H. / Hudock, M.P. / Jeng, W.Y. / Chen, C.K.M. / Zhang, Y. / Song, Y. / Kuo, C.J. / Yin, F. / Oldfield, E. / Wang, A.H.J.
History
DepositionJan 24, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Undecaprenyl pyrophosphate synthetase
B: Undecaprenyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3135
Polymers56,9622
Non-polymers1,3513
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-28 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.973, 68.290, 110.234
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 Undecaprenyl pyrophosphate synthetase / UPP synthetase / Di-trans / poly-cis-decaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS


Mass: 28481.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET32/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-B76 / [1-HYDROXY-2-(1,1':3',1''-TERPHENYL-3-YLOXY)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)


Mass: 450.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H20O8P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% Ethylene glycol, 2-5% PEG35K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 17035 / Num. obs: 16798 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Redundancy: 7.77 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 41.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.18 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1639 / % possible all: 97.1

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JP3

1jp3


Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 809 -RANDOM
Rwork0.224 ---
all-17035 --
obs-16326 95.8 %-
Displacement parametersBiso mean: 57.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 90 206 3763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection
Rfree0.403 85
Rwork0.297 -
obs-1538

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