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- PDB-9ekn: Thomasclavelia ramosa Immunoglobulin A Protease Middle (Protease)... -

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Basic information

Entry
Database: PDB / ID: 9ekn
TitleThomasclavelia ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-terminal Domain #1 (Metal Chelated and Zinc Supplemented)
ComponentsIgA protease
KeywordsHYDROLASE / M64 protease / secreted protein / immune modulating / zinc metalloprotease
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
Biological speciesThomasclavelia ramosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsTran, N. / Frenette, A. / Holyoak, T.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structure of the Thomasclavelia ramosa immunoglobulin A protease reveals a modular and minimizable architecture distinct from other immunoglobulin A proteases.
Authors: Tran, N. / Frenette, A. / Holyoak, T.
History
DepositionDec 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgA protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7904
Polymers62,5971
Non-polymers1933
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.132, 85.644, 92.124
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: 62597.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thomasclavelia ramosa (bacteria) / Gene: iga / Production host: Escherichia coli B (bacteria) / References: UniProt: Q9AES2
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, pH 6.5 + 25% (w/v) PEG 3350 + 10 mM praseodymium (III) acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1808 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.78→92.01 Å / Num. obs: 54207 / % possible obs: 100 % / Redundancy: 12.71 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11
Reflection shellResolution: 1.78→1.81 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2637 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→62.73 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 2713 5.01 %
Rwork0.1707 --
obs0.1725 54106 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→62.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 6 489 4901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.37371430.34482605X-RAY DIFFRACTION99
1.82-1.850.35181490.30372661X-RAY DIFFRACTION100
1.85-1.890.2721640.25482629X-RAY DIFFRACTION100
1.89-1.930.28661320.23282686X-RAY DIFFRACTION100
1.93-1.980.2521510.21752681X-RAY DIFFRACTION100
1.98-2.030.27411640.20452641X-RAY DIFFRACTION100
2.03-2.080.24931460.20522663X-RAY DIFFRACTION100
2.08-2.140.23441310.18652710X-RAY DIFFRACTION100
2.14-2.210.20961470.16832675X-RAY DIFFRACTION100
2.21-2.290.2281640.1752691X-RAY DIFFRACTION100
2.29-2.380.25641140.17652711X-RAY DIFFRACTION100
2.38-2.490.21381190.17362705X-RAY DIFFRACTION100
2.49-2.620.26281290.18582721X-RAY DIFFRACTION100
2.62-2.780.22391510.18882713X-RAY DIFFRACTION100
2.78-30.24791140.19282741X-RAY DIFFRACTION100
3-3.30.21491420.16892740X-RAY DIFFRACTION100
3.3-3.780.18781490.15522732X-RAY DIFFRACTION100
3.78-4.760.13571490.12512780X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / 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)
12.51460.62130.04061.65810.05740.8569-0.0267-0.0026-0.0047-0.00080.02890.22610.0272-0.0707-0.00720.20690.0195-0.00890.1881-0.02940.1995-5.97679.385821.0158
22.57530.09650.30422.06940.19271.6822-0.0818-0.60440.02220.53040.0832-0.18470.0773-0.07610.00460.33040.0557-0.06370.3155-0.04810.199620.28089.616136.8928
32.01550.2290.51781.70920.06240.8507-0.0886-0.03670.19850.11740.0899-0.444-0.06240.06860.00340.22920.0281-0.02610.2209-0.05030.253527.621819.95724.6609
45.50652.36973.69264.02692.94134.0752-0.32410.66470.0791-0.82650.30740.2152-0.21460.14180.01270.4058-0.0665-0.02570.30430.04430.25677.748528.03437.1713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 564 )
2X-RAY DIFFRACTION2chain 'A' and (resid 565 through 674 )
3X-RAY DIFFRACTION3chain 'A' and (resid 675 through 830 )
4X-RAY DIFFRACTION4chain 'A' and (resid 831 through 876 )

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