[English] 日本語
Yorodumi
- PDB-5cqj: Crystal structure of E. coli undecaprenyl pyrophosphate synthase ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more