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- PDB-2d2r: Crystal structure of Helicobacter pylori Undecaprenyl Pyrophospha... -

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Basic information

Entry
Database: PDB / ID: 2d2r
TitleCrystal structure of Helicobacter pylori Undecaprenyl Pyrophosphate Synthase
ComponentsUndecaprenyl Pyrophosphate Synthase
KeywordsTRANSFERASE / prenyl / prenyltransferase / undecaprenyl
Function / homology
Function and homology information


ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / magnesium ion binding / 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
Isoprenyl transferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsKuo, C.J. / Guo, R.T. / Chen, C.L. / Ko, T.P. / Cheng, Y.S. / Cheng, Y.L. / Liang, P.H. / Wang, A.H.-J.
CitationJournal: J.Biomed.Biotechnol. / Year: 2008
Title: Structure-based inhibitors exhibit differential activities against Helicobacter pylori and Escherichia coli undecaprenyl pyrophosphate synthases.
Authors: Kuo, C.J. / Guo, R.T. / Lu, I.L. / Liu, H.G. / Wu, S.Y. / Ko, T.P. / Wang, A.H. / Liang, P.H.
History
DepositionSep 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Undecaprenyl Pyrophosphate Synthase
B: Undecaprenyl Pyrophosphate Synthase


Theoretical massNumber of molelcules
Total (without water)57,1522
Polymers57,1522
Non-polymers00
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-22 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.630, 58.914, 153.425
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 Synthase


Mass: 28575.924 Da / Num. of mol.: 2 / Mutation: C234A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC43504 / Plasmid: pET32 Xa/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P55984, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 1.965 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: KSCN, PEG600, PEG5KMME, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 11, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→25 Å / Num. all: 37471 / Num. obs: 35917 / % possible obs: 95.59 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.7
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3338 / % possible all: 90.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X06

1x06


Resolution: 1.88→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1717 -RANDOM
Rwork0.1934 ---
all-37471 --
obs-34629 92.4 %-
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.88→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 0 581 4035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0193
X-RAY DIFFRACTIONc_angle_deg1.817
LS refinement shellResolution: 1.88→1.95 Å
RfactorNum. reflection% reflection
Rfree0.3 140 -
Rwork0.229 --
obs-3038 83.18 %

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