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- PDB-7pol: Crystal structure of profragilysin-3 (proBFT-3) from Bacteroides ... -

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Basic information

Entry
Database: PDB / ID: 7pol
TitleCrystal structure of profragilysin-3 (proBFT-3) from Bacteroides fragilis in complex with flumequine
ComponentsBFT-3
KeywordsHYDROLASE / protease / zymogen / proteolysis / enterotoxin / fragilysin
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Fragilysin / Fragilysin, N-terminal / Fragilysin, N-terminal domain superfamily / N-terminal domain of fragilysin / Metallo-peptidase family M12B Reprolysin-like / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-7X9 / PROLINE / BFT-3
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEckhard, U. / Guevara, T. / Gomis-Ruth, F.X.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2019-107725RG-I00 Spain
Citation
Journal: Protein Sci. / Year: 2022
Title: Repositioning small molecule drugs as allosteric inhibitors of the BFT-3 toxin from enterotoxigenic Bacteroides fragilis.
Authors: Jimenez-Alesanco, A. / Eckhard, U. / Asencio Del Rio, M. / Vega, S. / Guevara, T. / Velazquez-Campoy, A. / Gomis-Ruth, F.X. / Abian, O.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2011
Title: Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog.
Authors: Goulas, T. / Arolas, J.L. / Gomis-Ruth, F.X.
History
DepositionSep 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: BFT-3
B: BFT-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,38919
Polymers90,2792
Non-polymers2,11117
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, proBFT-3 monomer and dimer were observed on gelfitration at both low and high protein concentration. Immediate reinjection of the dimer lead to a dominantly dimeric ...Evidence: gel filtration, proBFT-3 monomer and dimer were observed on gelfitration at both low and high protein concentration. Immediate reinjection of the dimer lead to a dominantly dimeric chromatogram, indicating a certain dimer interface stability. The respective size exclusion chromatograms will be shown in the (to be published) paper.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-32 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.02, 84.02, 267.27
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BFT-3 / Metalloprotease / Metalloprotease enterotoxin


Mass: 45139.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ProBFT-3 (A18-D397) with a TEV-cleavable N-terminal His6-tag. Affinity tag was removed prior crystallization.
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: bft-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O86049

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Non-polymers , 6 types, 608 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-7X9 / (12~{R})-7-fluoranyl-12-methyl-4-oxidanylidene-1-azatricyclo[7.3.1.0^{5,13}]trideca-2,5(13),6,8-tetraene-3-carboxylic acid


Mass: 261.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12FNO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 20 % (w/v) PEG 3350 0.2 M ammonium sulfate Cryoprotection by soaking for 15-30 seconds in mother liquor supplemented with 2.5M L-proline.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.95→80.2 Å / Num. obs: 70841 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→1.97 Å / Num. unique obs: 2025 / CC1/2: 0.749

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p24

3p24


Resolution: 1.95→80.15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.215 716 -RANDOM
Rwork0.2013 ---
obs0.2014 70841 100 %-
Displacement parametersBiso mean: 41.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.7561 Å20 Å20 Å2
2---2.7561 Å20 Å2
3---5.5122 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.95→80.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 135 591 6087
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085629HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.897630HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2566SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes966HARMONIC5
X-RAY DIFFRACTIONt_it5629HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion722SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact5006SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.73
X-RAY DIFFRACTIONt_other_torsion2.65
LS refinement shellResolution: 1.95→1.97 Å
RfactorNum. reflection% reflection
Rfree0.221 24 -
Rwork0.2582 --
obs0.2577 2025 99.76 %
Refinement TLS params.

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)
11.8069-0.3244-0.55981.11970.0942.2770.027-0.1546-0.0054-0.1546-0.0809-0.0832-0.0054-0.08320.0540.00220.01120.0217-0.0082-0.0219-0.0102-11.797833.498-40.0851
21.9567-0.2712-0.32011.5594-0.35071.62270.12690.025-0.37660.025-0.0518-0.0882-0.3766-0.0882-0.07510.02710.04820.0432-0.04050.0082-0.072-18.773955.1036-34.0031
33.30530.5814-1.19572.1230.92997.12890.1366-0.0146-0.6074-0.0146-0.00720.5067-0.60740.5067-0.12940.0534-0.10280.02570.01330.0090.0099-0.998957.4004-34.4893
42.2176-0.0185-0.4772.10440.22321.80290.04890.1503-0.10230.1503-0.0352-0.1879-0.1023-0.1879-0.01380.01460.00030.02350.0376-0.016-0.0248-35.153235.8996-12.165
51.42940.27970.50722.3931-0.03581.46580.1030.01580.10660.0158-0.03880.060.10660.06-0.0642-0.0552-0.008-0.0212-0.0293-0.0009-0.064-23.26315.5439-14.3519
67.7646-2.1901-0.65895.9126-0.14045.1172-0.19530.78360.12830.78360.1543-0.17290.1283-0.17290.04110.1182-0.0112-0.10140.03170.0075-0.1113-20.492418.79692.9007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|34 - 193}
2X-RAY DIFFRACTION2{A|214 - 355}
3X-RAY DIFFRACTION3{A|356 - 397}
4X-RAY DIFFRACTION4{B|35 - 191}
5X-RAY DIFFRACTION5{B|213 - 355}
6X-RAY DIFFRACTION6{B|356 - 397}

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