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- PDB-7jli: Crystal structure of Bacillus subtilis UppS -

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Basic information

Entry
Database: PDB / ID: 7jli
TitleCrystal structure of Bacillus subtilis UppS
ComponentsIsoprenyl transferase
KeywordsTRANSFERASE / undecaprenyl / cis-prenyltransferase / carrier lipid
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
DI(HYDROXYETHYL)ETHER / Isoprenyl transferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

Deposited unit
A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9202
Polymers29,8141
Non-polymers1061
Water4,792266
1
A: Isoprenyl transferase
hetero molecules

A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8404
Polymers59,6282
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4910 Å2
ΔGint-9 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.539, 59.539, 161.798
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
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A063XDJ9, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3000, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→47.95 Å / Num. obs: 27983 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Net I/σ(I): 17.5 / Num. measured all: 343175
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
1.8-1.84132.4542084816050.5630.7042.5541.1100
9-47.95100.03129872990.9990.010.0325399.5

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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: 3WYI

3wyi


Resolution: 1.8→42.1 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 1430 5.13 %
Rwork0.1869 26467 -
obs0.1882 27897 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.67 Å2 / Biso mean: 40.6529 Å2 / Biso min: 21.65 Å2
Refinement stepCycle: final / Resolution: 1.8→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 7 266 2216
Biso mean--49.09 49.14 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.860.57391090.439526132722
1.86-1.940.31491400.289725652705
1.94-2.030.2881490.229625972746
2.03-2.130.24121460.217826032749
2.13-2.270.23791730.199125722745
2.27-2.440.18711240.197226272751
2.44-2.690.21061410.188226572798
2.69-3.080.21431560.190326362792
3.08-3.880.18521370.168827142851
3.88-42.10.19221550.161228833038
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)
12.03762.1511-1.19784.677-1.48923.6662-0.0117-0.0874-0.0333-0.1143-0.2024-0.86130.03291.18280.23020.2892-0.00250.00510.56880.09640.40269.733111.6086-33.159
24.9123-4.97614.90655.0312-4.97254.91140.04830.4504-0.2114-0.2764-0.1403-0.14310.85720.43890.18470.37020.01450.06020.36250.03730.3216-1.3628-4.6359-17.1772
38.31417.1209-6.61535.9973-5.70775.20120.4363-0.5727-0.22030.961-0.5375-0.4311-0.46960.8090.1640.4351-0.0326-0.0560.38180.00170.34643.2699.3931-18.25
43.0162.6572-2.07733.5657-3.84445.4031-0.3430.58640.0131-0.11510.75780.66170.6969-0.9499-0.43370.3602-0.10440.03710.3870.02120.4492-7.52478.8888-24.5229
55.46674.7425-2.80654.3376-3.39695.80310.1462-0.6004-0.08010.4721-0.09880.0616-0.37840.3872-0.08920.36070.0697-0.0270.38350.00310.3993-4.292613.8907-11.846
68.39372.5494-2.21223.11340.23875.20840.2429-0.43330.63690.2416-0.16190.0177-0.71190.3102-0.08610.3499-0.032-0.02410.25120.0060.2503-6.003222.648-19.6627
72.5656-2.08770.95362.8149-0.86921.4299-0.0855-0.07050.1630.0061-0.0156-0.1722-0.08280.05190.11340.2231-0.0401-0.00320.2169-0.00770.2227-10.481517.1479-35.9971
81.71381.8033-2.64022.1232-2.03657.6943-0.149-0.072-0.3545-0.1881-0.2348-0.20580.52570.5190.43010.26560.07010.04480.47940.06250.39210.22688.1011-39.6186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 41 )A20 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 52 )A42 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 73 )A53 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 92 )A74 - 92
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 116 )A93 - 116
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 160 )A117 - 160
7X-RAY DIFFRACTION7chain 'A' and (resid 161 through 239 )A161 - 239
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 260 )A240 - 260

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