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

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Basic information

Entry
Database: PDB / ID: 5cqj
TitleCrystal structure of E. coli undecaprenyl pyrophosphate synthase in complex with clomiphene
ComponentsDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Keywordstransferase/transferase INHIBITOR / transferase / cell wall / wall teichoic acid / antibacterial / transferase-transferase INHIBITOR complex
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
Clomifene / Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_database_related ...citation / pdbx_database_related / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_database_related.content_type ..._citation.journal_id_CSD / _pdbx_database_related.content_type / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Feb 12, 2020Group: Advisory / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)57,3683
Polymers56,9622
Non-polymers4061
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-11 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.312, 68.488, 111.630
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: 28481.127 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-53Q / Clomifene / 1-[(E)-2-chloro-1,2-diphenylethenyl]-4-methoxybenzene / clomiphene


Mass: 405.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28ClNO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.5, 0.16 M calcium acetate, 20 % PEG 8000, 20 % glycerol
PH range: 6.5

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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: 2.15→27.91 Å / Num. obs: 25369 / % possible obs: 94 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.052 / Net I/σ(I): 14.3 / Num. measured all: 84955
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
2.15-2.222.10.4522312115090.6780.3866.3
8.86-27.913.10.01664132042510.01195.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia20.3.11data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→26.507 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1253 4.95 %
Rwork0.1826 24074 -
obs0.1857 25327 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.5 Å2 / Biso mean: 33.2797 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 2.15→26.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 23 96 3417
Biso mean--55.18 30.93 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083392
X-RAY DIFFRACTIONf_angle_d1.0554579
X-RAY DIFFRACTIONf_chiral_restr0.041490
X-RAY DIFFRACTIONf_plane_restr0.005628
X-RAY DIFFRACTIONf_dihedral_angle_d14.2021245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1501-2.23610.31361150.25241841195666
2.2361-2.33780.2831270.23412333246083
2.3378-2.4610.28051440.212736288097
2.461-2.61510.26761330.19622783291699
2.6151-2.81680.24311330.19652819295299
2.8168-3.09980.26041190.19882859297899
3.0998-3.54750.27831250.17672875300099
3.5475-4.4660.22441690.153128583027100
4.466-26.5090.20321880.16492970315899
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)
11.5261-0.62550.48371.6949-1.09751.895-0.0450.14020.122-0.0805-0.1703-0.19220.14990.00980.21890.18970.00520.00020.1244-0.01260.1407-0.5852-0.703-1.8978
22.3616-2.43580.64377.7966-2.98622.4465-0.01730.25890.0452-0.40440.11170.03980.1795-0.3082-0.06830.1825-0.0067-0.00660.2902-0.0410.1807-6.385-3.6849-6.2219
31.23250.04050.35941.64070.50942.2632-0.0576-0.16390.0683-0.1777-00.5053-0.1224-0.83180.0040.2288-0.02540.00450.3877-0.00610.3417-17.0912-5.17594.4332
40.79970.0070.31340.8644-0.01361.4477-0.0194-0.1254-0.00730.1238-0.05990.09940.2057-0.18070.06080.1705-0.02930.04010.1634-0.00010.1855-2.73-4.173913.7809
52.3196-1.122-0.47842.75480.53831.6376-0.0664-0.2241-0.12620.04720.1792-0.28870.16310.4317-0.10120.15520.01840.01180.2287-0.01620.200523.79475.00821.8111
63.06041.66990.03553.9726-0.71751.79070.2633-0.6636-0.16410.2767-0.2682-0.430.00150.16170.01290.2228-0.0225-0.01290.2854-0.04830.199519.164910.055335.5544
71.05920.31590.37641.27040.62110.76290.0847-0.1060.05290.1123-0.08220.0274-0.0528-0.0894-0.02790.1644-0.01810.02550.1451-0.00570.12898.22117.312425.0456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 38 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 131 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 240 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 17 through 91 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 117 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 118 through 240 )B0

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