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- PDB-9qdh: Crystal structure of IgA protease (323-878) from Thomasclavelia ramosa -

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Basic information

Entry
Database: PDB / ID: 9qdh
TitleCrystal structure of IgA protease (323-878) from Thomasclavelia ramosa
ComponentsIgA protease
KeywordsHYDROLASE / IgA protease / peptidase / protease / IgA-P / M64 / metallopeptidase / metalloprotease / antibody / Ig / IgA / Thomasclavelia / metzincin / nephropathy / IgAN / hinge
Function / homology
Function and homology information


cellulose catabolic process / metallopeptidase activity / proteolysis / extracellular region / membrane
Similarity search - Function
Domain of unknown function DUF6273 / Domain of unknown function (DUF6273) / Peptidase M64, IgA / IgA Peptidase M64 / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Metallopeptidase, catalytic domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / IgA protease
Similarity search - Component
Biological speciesThomasclavelia ramosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMarquez-Monino, M.A. / Martinez Gascuena, A. / Aguillo-Urarte, M. / Manzanares-Gomez, A. / 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

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Assembly

Deposited unit
A: IgA protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9693
Polymers63,7981
Non-polymers1722
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint4 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.739, 85.198, 90.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IgA protease


Mass: 63797.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: M64 peptidase domain. Initial GGSG is a expression tag.
Source: (gene. exp.) Thomasclavelia ramosa (bacteria) / Gene: iga / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AES2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.14 Å3/Da / Density % sol: 42.68 % / Description: Rod
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris pH 8.5, 0.2M NaCl and VPCPVPSTPP peptide 5mM. Cryoprotectant solution: 30% glycerol, 27% PEG 3350, 0.1M Tris pH 8.5 and 0.2M NaCl. Protein:precipitant ratio 1:1. ...Details: 25% PEG 3350, 0.1M Tris pH 8.5, 0.2M NaCl and VPCPVPSTPP peptide 5mM. Cryoprotectant solution: 30% glycerol, 27% PEG 3350, 0.1M Tris pH 8.5 and 0.2M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 12.2 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: 0.61992 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 2→55.77 Å / Num. obs: 37731 / % possible obs: 99.95 % / Redundancy: 13.4 % / Biso Wilson estimate: 31.57 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.346 / Rpim(I) all: 0.098 / Net I/σ(I): 5.91
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.5 % / Rmerge(I) obs: 2.869 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 3740 / CC1/2: 0.534 / CC star: 0.835 / Rpim(I) all: 0.847 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→55.77 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 1807 4.79 %RANDOM
Rwork0.1941 ---
obs0.1965 37719 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→55.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 8 259 4727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034612
X-RAY DIFFRACTIONf_angle_d0.6236257
X-RAY DIFFRACTIONf_dihedral_angle_d5.038623
X-RAY DIFFRACTIONf_chiral_restr0.047659
X-RAY DIFFRACTIONf_plane_restr0.006815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.37181310.33712750X-RAY DIFFRACTION100
2.05-2.110.37571510.30632691X-RAY DIFFRACTION100
2.11-2.180.28291390.26822714X-RAY DIFFRACTION100
2.18-2.260.34211370.27752748X-RAY DIFFRACTION100
2.26-2.350.27391310.2392728X-RAY DIFFRACTION100
2.35-2.460.29991410.22062719X-RAY DIFFRACTION100
2.46-2.590.26241310.22252756X-RAY DIFFRACTION100
2.59-2.750.26831440.21062747X-RAY DIFFRACTION100
2.75-2.960.25981360.2082743X-RAY DIFFRACTION100
2.96-3.260.21921420.18962773X-RAY DIFFRACTION100
3.26-3.730.22781410.17332784X-RAY DIFFRACTION100
3.73-4.70.21761410.13962804X-RAY DIFFRACTION100
4.7-55.770.18481420.15952955X-RAY DIFFRACTION100

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