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- PDB-1v7u: Crystal structure of Undecaprenyl Pyrophosphate Synthase with far... -

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Basic information

Entry
Database: PDB / ID: 1v7u
TitleCrystal structure of Undecaprenyl Pyrophosphate Synthase with farnesyl pyrophosphate
ComponentsUndecaprenyl pyrophosphate synthetase
KeywordsTRANSFERASE / prenyltransferase / farnesyl pyrophosphate / isopentenyl pyrophosphate / substrate binding
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
FARNESYL DIPHOSPHATE / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 2.35 Å
AuthorsChang, S.-Y. / Ko, T.-P. / Chen, A.P.-C. / Wang, A.H.-J. / Liang, P.-H.
CitationJournal: Protein Sci. / Year: 2004
Title: Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies
Authors: Chang, S.-Y. / Ko, T.-P. / Chen, A.P.-C. / Wang, A.H.-J. / Liang, P.-H.
History
DepositionDec 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,1095
Polymers56,9622
Non-polymers1,1473
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-20 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.03, 69.20, 108.26
Angle α, β, γ (deg.)90, 90, 90
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) / Strain: Bos-12 / Plasmid: pET32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H28O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.07 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% ethylene glycol, 0.05% triton, 0.5mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %ethylene glycol1reservoirpH7.5
210 mg/mlprotein1drop
31 mMpeptide1drop
40.05 %Triton X-1001drop
50.5 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.35→10 Å / Num. all: 20047 / Num. obs: 19508 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 4.65 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 11
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.65 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 11 / Num. unique all: 19508 / % possible all: 97.1
Reflection
*PLUS
Num. measured all: 95659
Reflection shell
*PLUS
% possible obs: 95.1 % / Num. unique obs: 1882 / Num. measured obs: 9202 / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.35→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 927 -random
Rwork0.173 ---
obs0.254 19026 97.1 %-
all-20047 --
Refine analyze
FreeObs
Luzzati sigma a0.19 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 58 456 4068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.87
LS refinement shellResolution: 2.35→2.43 Å
RfactorNum. reflection% reflection
Rfree0.332 36 -
Rwork0.215 --
obs-9202 95.1 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Num. reflection obs: 1786

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