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- PDB-9qdi: Crystal structure of BF3526 peptidase from Bacteroides fragilis i... -

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Basic information

Entry
Database: PDB / ID: 9qdi
TitleCrystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide
Components
  • Lipoprotein
  • Synthetic peptide SER-THR-PRO-PRO
KeywordsHYDROLASE / IgA protease / peptidase / protease / BF3526 / M64 / metallopeptidase / metalloprotease / antibody / Ig / IgA / Bacteroides / metzincin / nephropathy / IgAN / hinge / complex / substrate / product
Function / homology
Function and homology information


metallopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M64, N-terminal / Peptidase M64, N-terminal domain superfamily / Peptidase M64 N-terminus / Peptidase M64, IgA / IgA Peptidase M64 / Metallopeptidase, catalytic domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
1,4-BUTANEDIOL / HEXANE-1,6-DIOL / : / DI(HYDROXYETHYL)ETHER / N-PROPANOL / Lipoprotein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMartinez Gascuena, A. / Marquez-Monino, M.A. / Manzanares-Gomez, A. / Aguillo-Urarte, M. / Trastoy, B.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesMICINN grant (PID2021-122177NA-I00) Spain
CitationJournal: Embo J. / Year: 2025
Title: Molecular basis of Fab-dependent IgA antibody recognition by gut-bacterial metallopeptidases.
Authors: Marquez-Monino, M.A. / Martinez Gascuena, A. / Azzam, T. / Persson, A. / Manzanares-Gomez, A. / Aguillo-Urarte, M. / Brown, T.T. / Montero-Sagarminaga, A. / Lood, R. / Naegeli, A. / Connell, ...Authors: Marquez-Monino, M.A. / Martinez Gascuena, A. / Azzam, T. / Persson, A. / Manzanares-Gomez, A. / Aguillo-Urarte, M. / Brown, T.T. / Montero-Sagarminaga, A. / Lood, R. / Naegeli, A. / Connell, S.R. / Sastre, D.E. / Sundberg, E.J. / Trastoy, B.
History
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 10, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein
B: Lipoprotein
C: Lipoprotein
D: Lipoprotein
E: Lipoprotein
F: Lipoprotein
G: Lipoprotein
H: Lipoprotein
I: Synthetic peptide SER-THR-PRO-PRO
J: Synthetic peptide SER-THR-PRO-PRO
K: Synthetic peptide SER-THR-PRO-PRO
L: Synthetic peptide SER-THR-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,69859
Polymers370,79212
Non-polymers2,90547
Water24,7171372
1
A: Lipoprotein
C: Lipoprotein
I: Synthetic peptide SER-THR-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,40615
Polymers92,6983
Non-polymers70812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5893 Å2
ΔGint-69.3 kcal/mol
Surface area30867 Å2
MethodPISA
2
B: Lipoprotein
E: Lipoprotein
K: Synthetic peptide SER-THR-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,37414
Polymers92,6983
Non-polymers67611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5605 Å2
ΔGint-72.4 kcal/mol
Surface area30985 Å2
MethodPISA
3
D: Lipoprotein
H: Lipoprotein
J: Synthetic peptide SER-THR-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,39214
Polymers92,6983
Non-polymers69411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5756 Å2
ΔGint-73.4 kcal/mol
Surface area31173 Å2
MethodPISA
4
F: Lipoprotein
G: Lipoprotein
L: Synthetic peptide SER-THR-PRO-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,52516
Polymers92,6983
Non-polymers82613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-65.4 kcal/mol
Surface area31095 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.294, 99.435, 103.386
Angle α, β, γ (deg.)74.16, 88.13, 82.44
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Lipoprotein


Mass: 46148.824 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Initial GA is a expression tag
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF9343_3433 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5L9L3
#2: Protein/peptide
Synthetic peptide SER-THR-PRO-PRO


Mass: 400.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 8 types, 1419 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#9: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1372 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.43 % / Description: Plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris Bicine pH 8.5, 20% Ethylen glycol, 10% PEG 8000, 0.12 M 1,6-Hexanediol, 0.12 M 1-Butanol, 0.12 M 1,2-Propanediol, 0.12 M 2-Propanol, 0.12 M 1,4-Butanediol, 0.12 M 1,3- Propanediol ...Details: 0.1 M Tris Bicine pH 8.5, 20% Ethylen glycol, 10% PEG 8000, 0.12 M 1,6-Hexanediol, 0.12 M 1-Butanol, 0.12 M 1,2-Propanediol, 0.12 M 2-Propanol, 0.12 M 1,4-Butanediol, 0.12 M 1,3- Propanediol and VPCPVPSTPP peptide 5 mM. Protein:precipitant ratio 1:1. Protein concentration: 10 mg/ml. Protein buffer: 20mM Tris pH 7.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.939→29.64 Å / Num. obs: 271117 / % possible obs: 96.95 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.99 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07842 / Rpim(I) all: 0.04963 / Net I/σ(I): 8.67
Reflection shellResolution: 1.94→1.96 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.9386 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 8246 / CC1/2: 0.425 / CC star: 0.772 / Rpim(I) all: 0.587 / % possible all: 88.79

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
FAST_DPdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→29.64 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 13524 4.99 %RANDOM
Rwork0.1709 ---
obs0.1729 271073 96.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25694 0 225 1375 27294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126635
X-RAY DIFFRACTIONf_angle_d0.98936152
X-RAY DIFFRACTIONf_dihedral_angle_d17.6369671
X-RAY DIFFRACTIONf_chiral_restr0.0623887
X-RAY DIFFRACTIONf_plane_restr0.0114682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.33424150.28687852X-RAY DIFFRACTION89
1.96-1.980.31074540.26538618X-RAY DIFFRACTION97
1.98-2.010.31724440.25638502X-RAY DIFFRACTION97
2.01-2.030.2964200.24898628X-RAY DIFFRACTION97
2.03-2.060.28484800.24238551X-RAY DIFFRACTION97
2.06-2.090.2874310.24328541X-RAY DIFFRACTION97
2.09-2.120.28484460.22268694X-RAY DIFFRACTION97
2.12-2.150.26044600.22068613X-RAY DIFFRACTION97
2.15-2.180.29424360.21988558X-RAY DIFFRACTION97
2.18-2.220.26084420.21748670X-RAY DIFFRACTION97
2.22-2.260.2634850.22158554X-RAY DIFFRACTION96
2.26-2.30.25294610.20248619X-RAY DIFFRACTION97
2.3-2.340.254620.19248579X-RAY DIFFRACTION98
2.34-2.390.25135040.1938598X-RAY DIFFRACTION98
2.39-2.440.25264130.19318713X-RAY DIFFRACTION98
2.44-2.50.22644510.19178646X-RAY DIFFRACTION98
2.5-2.560.24764690.1868690X-RAY DIFFRACTION98
2.56-2.630.24344530.18948671X-RAY DIFFRACTION98
2.63-2.710.24284540.18548691X-RAY DIFFRACTION98
2.71-2.80.23584520.1798722X-RAY DIFFRACTION98
2.8-2.90.22374520.1788659X-RAY DIFFRACTION98
2.9-3.010.23364500.17978749X-RAY DIFFRACTION98
3.01-3.150.23464500.18148692X-RAY DIFFRACTION98
3.15-3.310.22484240.17768712X-RAY DIFFRACTION98
3.31-3.520.19544750.16068594X-RAY DIFFRACTION97
3.52-3.790.18454700.15528547X-RAY DIFFRACTION97
3.79-4.170.18414320.13818554X-RAY DIFFRACTION96
4.17-4.780.15434670.1238522X-RAY DIFFRACTION97
4.78-6.010.16624400.13198497X-RAY DIFFRACTION96
6.01-29.640.17564320.15318313X-RAY DIFFRACTION94

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