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- PDB-7jlj: Crystal structure of Bacillus subtilis UppS in complex with clomiphene -

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Basic information

Entry
Database: PDB / ID: 7jlj
TitleCrystal structure of Bacillus subtilis UppS in complex with clomiphene
ComponentsIsoprenyl transferase
KeywordsTRANSFERASE / undecaprenyl / cis-prenyltransferase / carrier lipid / clomiphene
Function / homology
Function and homology information


Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / magnesium ion binding
Similarity search - Function
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
Similarity search - Domain/homology
Clomifene / Isoprenyl transferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWorkman, S.D. / Strynadka, N.C.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structural Insights into the Inhibition of Undecaprenyl Pyrophosphate Synthase from Gram-Positive Bacteria.
Authors: Workman, S.D. / Day, J. / Farha, M.A. / El Zahed, S.S. / Bon, C. / Brown, E.D. / Organ, M.G. / Strynadka, N.C.J.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2202
Polymers29,8141
Non-polymers4061
Water181
1
A: Isoprenyl transferase
hetero molecules

A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4404
Polymers59,6282
Non-polymers8122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.501, 58.501, 161.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Isoprenyl transferase / Undecaprenyl pyrophosphate synthase


Mass: 29814.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: uppS, A3772_08985, B4122_2664, B4417_3501, BS16045_01759, ETA10_09020, ETK61_09295, GII79_08795, SC09_Contig19orf01203
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A063XDJ9, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: PEG 3000, NaCitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97952 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 3.1→47.41 Å / Num. obs: 5598 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.109 / Rrim(I) all: 0.335 / Net I/σ(I): 8 / Num. measured all: 50706
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.319.51.45792649730.9050.4911.5392.299.9
8.77-47.417.20.04321312940.9990.0170.04628.499.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JLI

7jli


Resolution: 3.1→47.41 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 566 10.21 %
Rwork0.2209 4975 -
obs0.2264 5541 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.64 Å2 / Biso mean: 64.8393 Å2 / Biso min: 20.95 Å2
Refinement stepCycle: final / Resolution: 3.1→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 29 1 1929
Biso mean--65.13 33.33 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.410.38751440.30761187133199
3.41-3.910.30671400.23531209134999
3.91-4.920.24371210.185412591380100
4.92-47.410.22891610.210213201481100

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