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

ID or keywords:

Entry

Database: PDB / ID: 9ekk

Title

Thomasclavelia ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-terminal Domain #1 (Crystallized as Purified)

Components

IgA protease

Keywords

HYDROLASE / 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

Biological species

Thomasclavelia ramosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Tran, N. / Frenette, A. / Holyoak, T.

Funding support

1items

Citation

Journal: 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

Deposition	Dec 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ekk.cif.gz	478 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9ekk_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	9ekk_full_validation.pdf.gz	3.5 MB	Display
Data in XML	9ekk_validation.xml.gz	59.9 KB	Display
Data in CIF	9ekk_validation.cif.gz	86.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ek/9ekk ftp://data.pdbj.org/pub/pdb/validation_reports/ek/9ekk	HTTPS FTP

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Related structure data

Related structure data	9ekmC 9eknC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#28 - Apr 2002 Anthrax Toxin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: IgA protease

B: IgA protease

hetero molecules

126 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: IgA protease

hetero molecules

defined by author
Evidence: SAXS, gel filtration
62.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: IgA protease

hetero molecules

defined by author
62.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.689, 91.270, 86.860
Angle α, β, γ (deg.)	90.00, 91.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	IgA protease Mass: 62597.453 Da / Num. of mol.: 2 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.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PR / PRASEODYMIUM ION Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1264 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.12 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1808 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 21, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1808 Å / Relative weight: 1
Reflection	Resolution: 1.65→91.45 Å / Num. obs: 122442 / % possible obs: 92.39 % / Redundancy: 6.57 % / CC_1/2: 0.997 / R_merge(I) obs: 0.083 / Net I/σ(I): 14.4
Reflection shell	Resolution: 1.65→1.67 Å / R_merge(I) obs: 1.41 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 21824 / CC_1/2: 0.591

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
DIALS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→55.34 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2307	6315	5.2 %
R_work	0.1959	-	-
obs	0.1977	121390	91.6 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.65→55.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8812	0	6	1264	10082

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.65-1.67	0.3442	150	0.3069	2329	X-RAY DIFFRACTION	57
1.67-1.69	0.3449	131	0.3026	2664	X-RAY DIFFRACTION	63
1.69-1.71	0.3318	187	0.285	2955	X-RAY DIFFRACTION	72
1.71-1.73	0.3431	186	0.2801	3562	X-RAY DIFFRACTION	85
1.73-1.75	0.3164	208	0.2665	3776	X-RAY DIFFRACTION	91
1.75-1.78	0.3109	243	0.2511	3832	X-RAY DIFFRACTION	93
1.78-1.8	0.2891	249	0.2429	3894	X-RAY DIFFRACTION	95
1.8-1.83	0.3045	287	0.2333	3891	X-RAY DIFFRACTION	95
1.83-1.86	0.28	246	0.2212	3937	X-RAY DIFFRACTION	95
1.86-1.89	0.3709	210	0.3171	3838	X-RAY DIFFRACTION	92
1.89-1.92	0.5378	195	0.5309	3732	X-RAY DIFFRACTION	90
1.92-1.96	0.4034	174	0.3626	3732	X-RAY DIFFRACTION	89
1.96-1.99	0.2749	213	0.2051	4002	X-RAY DIFFRACTION	96
1.99-2.03	0.2258	238	0.1795	3992	X-RAY DIFFRACTION	96
2.03-2.08	0.1939	213	0.1752	4050	X-RAY DIFFRACTION	96
2.08-2.13	0.2357	219	0.1745	4002	X-RAY DIFFRACTION	96
2.13-2.18	0.2262	198	0.1867	4096	X-RAY DIFFRACTION	97
2.18-2.24	0.3773	153	0.3253	3696	X-RAY DIFFRACTION	88
2.24-2.3	0.4449	185	0.3749	3661	X-RAY DIFFRACTION	87
2.3-2.38	0.2311	216	0.1901	4057	X-RAY DIFFRACTION	97
2.38-2.46	0.2437	182	0.1741	4130	X-RAY DIFFRACTION	97
2.46-2.56	0.241	230	0.1729	4079	X-RAY DIFFRACTION	97
2.56-2.68	0.2045	209	0.166	4104	X-RAY DIFFRACTION	98
2.68-2.82	0.2069	196	0.1695	4133	X-RAY DIFFRACTION	98
2.82-3	0.1993	193	0.1722	4146	X-RAY DIFFRACTION	98
3-3.23	0.1912	219	0.1628	4154	X-RAY DIFFRACTION	98
3.23-3.55	0.1977	273	0.1538	4084	X-RAY DIFFRACTION	99
3.55-4.07	0.1728	230	0.1598	4109	X-RAY DIFFRACTION	98
4.07-5.12	0.136	247	0.125	4189	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.7896	-0.0201	-0.6299	0.6106	0.0658	1.2073	0.0027	-0.0827	-0.0469	-0.0502	-0.0018	-0.0844	0.019	0.1792	-0.0035	0.1134	0.011	-0.002	0.1923	-0.0037	0.1233	-9.669	-5.764	11.616
2	3.2802	-0.8452	0.0604	1.3656	0.1621	0.9883	0.0822	0.2327	0.287	-0.2664	-0.0786	0.023	-0.158	-0.0024	0.0175	0.184	-0.0225	0.0272	0.1966	0.0053	0.1637	-20.625	6.518	6.237
3	1.2542	-0.3907	-0.5192	1.1153	0.1924	0.9219	0.0503	0.006	0.1227	-0.0539	0.0124	-0.0133	-0.0931	0.0131	-0.0648	0.1455	-0.008	-0.003	0.1676	-0.0008	0.1704	-40.071	13.126	12.347
4	1.1977	-0.6005	-0.1329	0.5983	0.0755	0.527	-0.0487	-0.1125	-0.1401	0.0417	0.0415	0.0375	0.0538	-0.0066	0.0083	0.1667	-0.0227	0.0185	0.1962	0.0182	0.198	-39.935	-4.832	22.45
5	1.7896	0.2183	0.6908	0.8051	0.0906	1.6355	-0.0136	-0.0299	0.0966	-0.0238	-0.0471	0.1548	-0.0786	-0.2536	0.0609	0.1563	0.037	0.0188	0.228	0.003	0.1382	-25.817	3.546	-32.149
6	3.3154	-0.6998	0.3202	1.3807	-0.0595	0.1331	0.1174	0.223	-0.1564	-0.1857	-0.105	-0.0087	0.1483	0.065	-0.0122	0.1917	0.0039	-0.0113	0.2274	0.0154	0.1415	-14.514	-8.382	-37.073
7	1.5255	-0.6839	0.3552	2.472	0.3646	1.086	0.0255	0.0906	-0.1717	0.0393	0.0931	-0.0181	0.1839	0.165	-0.1101	0.1541	0.0215	-0.0014	0.2108	-0.0036	0.1245	3.139	-14.206	-32.713
8	1.0248	-0.2532	0.4941	0.489	-0.0569	0.9606	0.0063	0.0294	0.0507	0.0288	0.004	-0.0173	-0.0134	0.1393	-0.0162	0.1865	-0.0163	0.006	0.1745	0.0087	0.1465	5.057	1.494	-19.646

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 330:480 )	A	330 - 480
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 481:534 )	A	481 - 534
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 535:661 )	A	535 - 661
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 662:846 )	A	662 - 846
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 330:480 )	B	330 - 480
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 481:534 )	B	481 - 534
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 535:644 )	B	535 - 644
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 645:846 )	B	645 - 846

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