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- PDB-5cqb: Crystal structure of E. coli undecaprenyl pyrophosphate synthase -

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Basic information

Entry
Database: PDB / ID: 5cqb
TitleCrystal structure of E. coli undecaprenyl pyrophosphate synthase
ComponentsDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
KeywordsTRANSFERASE / cell wall / wall teichoic acid / antibacterial
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
TRIETHYLENE GLYCOL / 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: 2.2 Å
AuthorsWorrall, L.J. / Conrady, D.G. / Strynadka, N.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Antagonism screen for inhibitors of bacterial cell wall biogenesis uncovers an inhibitor of undecaprenyl diphosphate synthase.
Authors: Farha, M.A. / Czarny, T.L. / Myers, C.L. / Worrall, L.J. / French, S. / Conrady, D.G. / Wang, Y. / Oldfield, E. / Strynadka, N.C. / Brown, E.D.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation.journal_id_CSD / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
B: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8503
Polymers56,7002
Non-polymers1501
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-11 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.981, 68.229, 111.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) / Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / ...Ditrans / polycis-undecaprenylcistransferase / Undecaprenyl diphosphate synthase / UDS / Undecaprenyl pyrophosphate synthase / UPP synthase


Mass: 28349.932 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ispU, rth, uppS, yaeS, b0174, JW0169 / Production host: Escherichia coli (E. coli)
References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 41.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M lithium sulfate, 0.1 M ADA 6.5, 12 % w/v PEG 4K, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→46.28 Å / Num. obs: 25073 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 32.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.06 / Net I/σ(I): 13 / Num. measured all: 134678
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.2-2.275.41.1421.81149421360.5840.527100
9.07-46.284.40.02453.218284190.9990.01398.6

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.279 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 1218 4.87 %
Rwork0.1917 23799 -
obs0.1943 25017 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.76 Å2 / Biso mean: 40.73 Å2 / Biso min: 15.18 Å2
Refinement stepCycle: final / Resolution: 2.2→46.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 10 74 3379
Biso mean--58.34 37.55 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083380
X-RAY DIFFRACTIONf_angle_d1.0314563
X-RAY DIFFRACTIONf_chiral_restr0.042490
X-RAY DIFFRACTIONf_plane_restr0.004601
X-RAY DIFFRACTIONf_dihedral_angle_d14.1611226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.28810.32311420.256125852727
2.2881-2.39220.27691350.239925882723
2.3922-2.51830.27291330.221926342767
2.5183-2.67610.27221200.214326132733
2.6761-2.88270.23251150.206226312746
2.8827-3.17270.3431110.208226602771
3.1727-3.63170.23931220.178626582780
3.6317-4.57490.21661630.158926652828
4.5749-46.28870.21621770.180627652942
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3628-0.1845-0.55350.1409-0.21450.4423-0.04810.2058-0.07930.0762-0.09830.02210.1293-0.054-0.00030.2869-0.0002-0.04520.2495-0.00490.241359.863266.0558107.6144
20.24970.17510.25240.3779-0.12520.38150.0904-0.16570.14020.0719-0.2040.29720.1742-0.6208-0.00080.2899-0.04830.0070.4074-0.0310.370147.199862.313116.4337
30.6860.02850.22251.0312-0.0710.76470.0316-0.0631-0.0746-0.0064-0.07310.11570.183-0.049900.2305-0.02740.01870.21930.00470.264461.257264.6804125.8751
40.35770.0314-0.01450.39730.29510.82060.0068-0.1151-0.0857-0.1690.10260.0105-0.08490.218-0.00010.1889-0.00120.02050.2476-0.00310.232786.415673.7095132.5228
50.1004-0.04190.02470.0217-0.00960.028-0.2432-0.2364-0.2756-0.37960.0137-0.54410.56510.9527-0.00880.45120.17320.03760.536-0.05390.463987.954678.156146.7335
60.69120.43930.80361.59770.54680.60910.0886-0.10470.07220.1161-0.10260.0619-0.028-0.0468-0.00140.2001-0.01590.03510.2024-0.02190.184571.895275.6153137.6673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 146 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 239 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 87 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 88 through 102 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 238 )B0

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