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- PDB-7jlm: Crystal structure of Bacillus subtilis UppS in complex with MAC-0... -

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Basic information

Entry
Database: PDB / ID: 7jlm
TitleCrystal structure of Bacillus subtilis UppS in complex with MAC-0547630
ComponentsIsoprenyl transferase
KeywordsTRANSFERASE / undecaprenyl / cis-prenyltransferase / carrier lipid / MAC-0547630
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
CITRIC ACID / Chem-V07 / Isoprenyl transferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
B: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6616
Polymers59,6282
Non-polymers1,0334
Water1,44180
1
A: Isoprenyl transferase
hetero molecules

A: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6616
Polymers59,6282
Non-polymers1,0334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4380 Å2
ΔGint-10 kcal/mol
Surface area20530 Å2
MethodPISA
2
B: Isoprenyl transferase
hetero molecules

B: Isoprenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6616
Polymers59,6282
Non-polymers1,0334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4160 Å2
ΔGint-14 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.724, 87.400, 159.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Isoprenyl transferase / Undecaprenyl pyrophosphate synthase


Mass: 29814.117 Da / Num. of mol.: 2
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-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-V07 / 7-(azepan-1-yl)-3-(4-fluorophenyl)-5-methylpyrazolo[1,5-a]pyrimidine / MAC-0547630


Mass: 324.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21FN4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.5 Å3/Da / Density % sol: 50.75 % / Mosaicity: 0 °
Crystal growTemperature: 294 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: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→79.51 Å / Num. obs: 26950 / % possible obs: 100 % / Redundancy: 23.6 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.023 / Rrim(I) all: 0.111 / Net I/σ(I): 16.1 / Num. measured all: 637138 / Scaling rejects: 61
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
2.3-2.3823.50.986119626000.9530.2051.0023.1100
8.91-79.5121.20.0441128053210.010.04560.499.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JLI

7jli


Resolution: 2.3→79.51 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 33.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1374 5.12 %
Rwork0.1945 25458 -
obs0.1973 26832 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.44 Å2 / Biso mean: 73.0344 Å2 / Biso min: 29.44 Å2
Refinement stepCycle: final / Resolution: 2.3→79.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 74 80 3964
Biso mean--75.35 63.52 -
Num. residues----472
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.380.4159960.34125442640100
2.38-2.480.30391100.30682514262499
2.48-2.590.34361360.26725182654100
2.59-2.730.32111510.25962483263499
2.73-2.90.30131410.251725332674100
2.9-3.120.32811280.243525392667100
3.12-3.440.29781360.229725502686100
3.44-3.930.26411520.184925392691100
3.93-4.950.20921810.145125392720100
4.96-79.510.18751430.154126992842100
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)
13.34022.27731.20084.38220.31276.97750.0235-0.25930.21370.4453-0.13970.4192-0.9065-0.26940.1120.5280.12730.06950.7787-0.06130.3126-7.8879-4.4998-24.3456
27.4683-0.276-1.82116.1847-0.53026.38080.2035-0.2643-0.15981.0545-0.36280.2590.0428-0.46010.13580.6391-0.09550.0820.93990.00550.3317-10.5824-16.9909-16.681
30.7255-0.8099-0.20897.47940.82412.5056-0.1081-0.0001-0.00370.44780.05940.423-0.1514-0.39750.06070.28970.01870.00170.9131-0.02240.3021-6.4436-15.7285-35.8232
43.53913.0346-0.99476.8147-3.66616.9559-0.19290.4241-0.2292-0.15320.0237-0.23440.24760.39580.13630.60070.07250.04280.6256-0.06470.330437.0882-6.1795-16.4044
54.9712-1.70751.37988.732-0.5257.0865-0.3931.1612-0.0273-0.20720.17350.05980.5582-0.21060.2380.6566-0.20550.05880.9377-0.12680.338224.5884-8.2869-24.2511
63.5334-0.0212-0.29920.80230.01642.6817-0.08850.4798-0.28910.1098-0.0479-0.06390.21350.20710.15710.70640.00340.01160.3841-0.00830.293325.7684-5.962-4.6804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 92 )A20 - 92
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 160 )A93 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 255 )A161 - 255
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 92 )B20 - 92
5X-RAY DIFFRACTION5chain 'B' and (resid 93 through 160 )B93 - 160
6X-RAY DIFFRACTION6chain 'B' and (resid 161 through 255 )B161 - 255

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