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- PDB-1jp3: Structure of E.coli undecaprenyl pyrophosphate synthase -

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Basic information

Entry
Database: PDB / ID: 1jp3
TitleStructure of E.coli undecaprenyl pyrophosphate synthase
Componentsundecaprenyl pyrophosphate synthase
KeywordsTRANSFERASE / Rossmann fold / hydrophobic tunnel / product chain length / flexible loop
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 / 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] / di-trans,poly-cis-undecaprenyl-diphosphate synthase 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 / cytosol / cytoplasm
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
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / single-wavelength anomalous diffraction (SAD) / Resolution: 1.8 Å
AuthorsKo, T.P. / Chen, Y.K. / Robinson, H. / Tsai, P.C. / Gao, Y.G. / Chen, A.P.C. / Wang, A.H.J. / Liang, P.H.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis.
Authors: Ko, T.P. / Chen, Y.K. / Robinson, H. / Tsai, P.C. / Gao, Y.G. / Chen, A.P. / Wang, A.H. / Liang, P.H.
History
DepositionJul 31, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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 synthase
B: undecaprenyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9403
Polymers57,3372
Non-polymers6031
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-9 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.180, 67.334, 110.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe enzyme is a dimer, including chains A and B in the asymmetric unit.

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Components

#1: Protein undecaprenyl pyrophosphate synthase


Mass: 28668.705 Da / Num. of mol.: 2 / Mutation: M25MSE/M86MSE/M176MSE/M183MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET32XA-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-EGC / 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL / TRITON X-100


Mass: 602.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58O10 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 40.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Triton X-100, PEG8000, ethylele glycol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.1 %Triton X-1001drop
325 %PEG4001reservoir
4100 mMsodium cacodylate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 13, 2000
RadiationMonochromator: Silicon channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 44972 / Num. obs: 44820 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 10.1 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 25.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 6.5 / Num. unique all: 4426 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 4420

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Processing

Software
NameVersionClassification
SOLVEphasing
RESOLVEmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: single-wavelength anomalous diffraction (SAD)
Resolution: 1.8→19.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 533864.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2215 5 %RANDOM
Rwork0.194 ---
all0.1953 44367 --
obs0.194 44367 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.2753 Å2 / ksol: 0.349888 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---1.2 Å20 Å2
3---1.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-6 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 12 645 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.562
X-RAY DIFFRACTIONc_scangle_it2.352.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 199 4.6 %
Rwork0.236 4115 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3EGC.PARAMEGC.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_scbond_it1.562
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scangle_it2.352.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.247 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.236

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