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

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Basic information

Entry
Database: PDB / ID: 7pnd
TitleCrystal structure of profragilysin-3 (proBFT-3) from Bacteroides fragilis at 1.85 A resolution.
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
FORMIC ACID / PROLINE / BFT-3
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 6, 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)92,06325
Polymers90,2792
Non-polymers1,78423
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration at both high (~7 mg/ml) and low (~0.7 mg/ml) protein concentration showed a monomeric and dimeric peak. Furthermore, immediate reinjection of the later lead ...Evidence: gel filtration, Gel filtration at both high (~7 mg/ml) and low (~0.7 mg/ml) protein concentration showed a monomeric and dimeric peak. Furthermore, immediate reinjection of the later lead to a predominantly dimeric size exclusion profile. Additional evidence comes from crystallization in different space groups but which all have the same dimer as a building block. This information will be part of the accompanying paper which we hope to publish by end of the year.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint6 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.72, 82.74, 158.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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, 750 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 18% (w/v) PEG3350, 0.2 M magnesium formate, pH 5.9.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.85→63.07 Å / Num. obs: 78068 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 13.4
Reflection shellResolution: 1.85→1.87 Å / Num. unique obs: 2110 / CC1/2: 0.706

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p24

3p24


Resolution: 1.85→63.07 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 748 -RANDOM
Rwork0.1886 ---
obs0.1888 78068 100 %-
Displacement parametersBiso mean: 37.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.5808 Å20 Å20 Å2
2---1.1451 Å20 Å2
3---1.7259 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.85→63.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 105 727 6408
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085830HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.917889HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2675SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1008HARMONIC5
X-RAY DIFFRACTIONt_it5830HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion760SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact6161SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion2.63
LS refinement shellResolution: 1.85→1.87 Å
RfactorNum. reflection% reflection
Rfree0.3934 17 -
Rwork0.3056 --
obs0.3062 2110 99.62 %
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)
11.01730.20870.30431.27340.32631.87670.00440.05790.33390.05790.0011-0.18260.3339-0.1826-0.00560.0513-0.04040.02810.01220.01010.0549.5981-16.7713-38.1345
21.4163-0.47790.19071.0244-0.00271.4825-0.04890.0541-0.03540.05410.05090.0297-0.03540.0297-0.002-0.02590.0084-0.0014-0.0144-0.004-0.013820.7027-5.8361-24.8521
31.20010.2902-0.1433.2708-0.87182.20870.01580.1-0.01710.1-0.0905-0.3209-0.0171-0.32090.0747-0.07160.02520.01640.0277-0.0173-0.02754.9883-3.8628-19.0738
41.55210.3795-0.17341.0167-0.12141.33850.00990.0058-0.0330.0058-0.04680.1767-0.0330.17670.0368-0.0028-0.01930.01190.03750.02210.029331.81694.6269-55.8096
51.2388-0.13680.21451.63070.03352.24390.0267-0.15740.1775-0.1574-0.01170.01950.17750.0195-0.0150.0106-0.00680.00850.0076-0.0126-0.063816.4431-2.3312-69.3704
62.0031-0.97790.77821.530.28242.1058-0.0074-0.1529-0.3078-0.1529-0.10280.0333-0.30780.03330.11020.03920.00320.0132-0.00580.06230.006315.237614.9883-71.5041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|34 - 207}
2X-RAY DIFFRACTION2{A|208 - 355 A|999 - 999}
3X-RAY DIFFRACTION3{A|356 - 397}
4X-RAY DIFFRACTION4{B|34 - 200}
5X-RAY DIFFRACTION5{B|216 - 355 B|999 - 999}
6X-RAY DIFFRACTION6{B|356 - 397}

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