[English] 日本語
Yorodumi
- PDB-9qdi: Crystal structure of BF3526 peptidase from Bacteroides fragilis i... -

+
Open data


ID or keywords:

Loading...

-
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: To Be Published
Title: Structural insights into IgA recognition by M64 peptidases
Authors: Marquez-Monino, M.A. / Martinez Gascuena, A. / Azzam, T. / Persson, A. / Manzanares-Gomez, A. / Aguillo-Urarte, M. / Brown, T.T. / Montero, A. / Lood, R. / Naegali, A. / Du, J.J. / Connell, ...Authors: Marquez-Monino, M.A. / Martinez Gascuena, A. / Azzam, T. / Persson, A. / Manzanares-Gomez, A. / Aguillo-Urarte, M. / Brown, T.T. / Montero, A. / Lood, R. / Naegali, A. / Du, J.J. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more