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- PDB-2e99: E. coli undecaprenyl pyrophosphate synthase in complex with BPH-608 -

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Basic information

Entry
Database: PDB / ID: 2.0E+99
TitleE. coli undecaprenyl pyrophosphate synthase in complex with BPH-608
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-B08 / 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 Å
AuthorsGuo, R.T. / Ko, T.P. / Cao, R. / 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)59,1347
Polymers56,9622
Non-polymers2,1725
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-42 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.292, 68.156, 109.906
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-B08 / (1-HYDROXY-1-PHOSPHONO-2-[1,1';3',1'']TERPHENYL-3-YL-ETHYL)-PHOSPHONIC ACID / [1-HYDROXY-2-(1,1':3',1''-TERPHENYL-3-YL)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)


Mass: 434.316 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H20O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
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→30 Å / Num. all: 33334 / Num. obs: 33217 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 7.93 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 36.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 5 / Num. unique all: 3267 / % possible all: 100

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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→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1611 -RANDOM
Rwork0.191 ---
all-33334 --
obs-32558 97.7 %-
Displacement parametersBiso mean: 37.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 145 270 3957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.274 139
Rwork0.213 -
obs-2969

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