PDB-8uen: Crystal structure of Corynebacterium ulcerans endo-beta-N-acetylg...

ID or keywords:

Entry

Database: PDB / ID: 8uen

Title

Crystal structure of Corynebacterium ulcerans endo-beta-N-acetylglucosaminidase catalytically inactive CU43 D187A-E189A at 2.3 A (P 21 21 2)

Components

Corynebacterial protease CP40

Keywords

HYDROLASE / Secreted Endo-beta-N-acetylglucosaminidase / CU43 / IgG-specific

Function / homology

:

Function and homology information

Biological species

Corynebacterium ulcerans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Sastre, D.E. / Sultana, N. / Sundberg, E.J.

Funding support

United States, 1items

Citation

Journal: Cell / Year: 2024
Title: Potent efficacy of an IgG-specific endoglycosidase against IgG-mediated pathologies.
Authors: Sastre, D.E. / Bournazos, S. / Du, J. / Boder, E.J. / Edgar, J.E. / Azzam, T. / Sultana, N. / Huliciak, M. / Flowers, M. / Yoza, L. / Xu, T. / Chernova, T.A. / Ravetch, J.V. / Sundberg, E.J.

History

Deposition	Oct 2, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 16, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: 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.title / _citation.year
Revision 1.2	Nov 6, 2024	Group: 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_author.name
Revision 1.3	Dec 11, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8uen.cif.gz	282.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8uen.ent.gz	227.8 KB	Display	PDB format
PDBx/mmJSON format	8uen.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8uen_validation.pdf.gz	444.9 KB	Display	wwPDB validaton report
Full document	8uen_full_validation.pdf.gz	450.4 KB	Display
Data in XML	8uen_validation.xml.gz	30.8 KB	Display
Data in CIF	8uen_validation.cif.gz	40.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ue/8uen ftp://data.pdbj.org/pub/pdb/validation_reports/ue/8uen	HTTPS FTP

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Related structure data

Related structure data	8uraC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Corynebacterial protease CP40

B: Corynebacterial protease CP40

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry, gel filtration

Unit cell

Length a, b, c (Å)	202.950, 58.762, 74.562
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-553- HOH
2	1	A-601- HOH

#1: Protein	Corynebacterial protease CP40 Mass: 46107.309 Da / Num. of mol.: 2 / Mutation: D187A, E189A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium ulcerans (bacteria) / Gene: cpp, CULC0211_20780 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A830QWM5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.86 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.12 M Ethylene glycols, 0.1 M Tri-BICINE pH8.5, 20% v/v PEG 500 MME; 10 % w/v PEG 20000 (Morpheus E9)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→50.74 Å / Num. obs: 74936 / % possible obs: 98 % / Redundancy: 13 % / R_pim(I) all: 0.094 / Net I/σ(I): 5.4
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 9.4 % / Num. unique obs: 2444 / CC_1/2: 0.391 / % possible all: 83

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→50.1 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2447	3742	5.04 %
R_work	0.2223	-	-
obs	0.2234	74307	97.06 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→50.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5259	0	0	258	5517

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5373
X-RAY DIFFRACTION	f_angle_d	0.506	7275
X-RAY DIFFRACTION	f_dihedral_angle_d	12.787	1959
X-RAY DIFFRACTION	f_chiral_restr	0.039	779
X-RAY DIFFRACTION	f_plane_restr	0.004	952

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 (%)
2.3-2.33	0.3921	115	0.3517	2145	X-RAY DIFFRACTION	78
2.33-2.36	0.3896	113	0.335	2197	X-RAY DIFFRACTION	83
2.36-2.39	0.3329	129	0.3253	2357	X-RAY DIFFRACTION	89
2.39-2.43	0.337	135	0.3145	2501	X-RAY DIFFRACTION	92
2.43-2.46	0.3177	140	0.3004	2585	X-RAY DIFFRACTION	96
2.46-2.5	0.2446	137	0.2851	2625	X-RAY DIFFRACTION	99
2.5-2.54	0.3447	139	0.2755	2679	X-RAY DIFFRACTION	99
2.54-2.59	0.2732	147	0.2786	2653	X-RAY DIFFRACTION	99
2.59-2.63	0.3116	139	0.2783	2641	X-RAY DIFFRACTION	99
2.63-2.68	0.3255	139	0.2786	2677	X-RAY DIFFRACTION	99
2.68-2.74	0.2825	142	0.2746	2641	X-RAY DIFFRACTION	99
2.74-2.8	0.2862	146	0.259	2711	X-RAY DIFFRACTION	99
2.8-2.86	0.2938	133	0.2635	2642	X-RAY DIFFRACTION	99
2.86-2.93	0.2889	143	0.2608	2685	X-RAY DIFFRACTION	99
2.93-3.01	0.3075	137	0.259	2645	X-RAY DIFFRACTION	99
3.01-3.1	0.3069	143	0.2529	2688	X-RAY DIFFRACTION	99
3.1-3.2	0.2207	144	0.2329	2656	X-RAY DIFFRACTION	99
3.2-3.32	0.2629	138	0.2338	2686	X-RAY DIFFRACTION	100
3.32-3.45	0.2273	145	0.2193	2696	X-RAY DIFFRACTION	99
3.45-3.61	0.2491	140	0.2047	2672	X-RAY DIFFRACTION	100
3.61-3.8	0.2092	149	0.1843	2709	X-RAY DIFFRACTION	100
3.8-4.03	0.209	142	0.1744	2636	X-RAY DIFFRACTION	100
4.03-4.35	0.184	145	0.1728	2726	X-RAY DIFFRACTION	100
4.35-4.78	0.1702	138	0.1658	2667	X-RAY DIFFRACTION	100
4.78-5.47	0.2139	139	0.1834	2693	X-RAY DIFFRACTION	100
5.47-6.89	0.2654	145	0.2034	2680	X-RAY DIFFRACTION	100
6.9-50.1	0.1722	140	0.1891	2672	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	2.5908	0.3858	0.0555	1.0993	0.4044	1.4087	-0.0528	0.5744	0.4959	-0.2419	0.0982	0.2098	-0.195	0.1974	-0.1066	0.2979	0.0158	0.0101	0.2416	0.1175	0.3269	25.978	8.561	28.057
2	5.0609	1.4105	-1.2293	6.7629	-2.8551	3.3912	0.0621	-1.1678	0.0643	1.0941	-0.0599	0.5327	0.2421	0.7564	0.0082	0.5357	0.0156	0.101	0.4571	-0.0354	0.3848	32.209	14.967	56.398
3	1.5018	0.4255	1.5247	1.6186	0.9295	1.265	-0.0091	0.0551	0.4626	0.0353	-0.0903	0.1421	-0.1217	-0.0989	0.0792	0.2783	0.02	0.0414	0.2662	0.0362	0.4146	25.249	16.041	43.123
4	3.6452	0.7654	0.5689	1.8403	0.4534	2.0921	-0.041	0.0461	0.0755	0.172	-0.1229	0.3374	0.0907	-0.3439	0.1328	0.2287	0.0081	0.0349	0.339	0.0484	0.3548	13.219	5.563	34.111
5	3.5966	-0.4179	-0.1327	0.9893	0.1942	2.5118	-0.0599	0.5193	0.1137	0.0617	-0.0427	0.1947	-0.0731	-0.0377	0.1005	0.2161	-0.0074	-0.0179	0.2887	0.0677	0.2542	23.095	5.52	27.757
6	2.8542	0.2787	1.5038	2.7912	1.2289	3.7416	0.1413	0.6091	-0.1816	-0.2115	-0.0769	-0.0533	0.2563	0.5008	-0.0084	0.2907	0.0617	0.0177	0.4587	0.0117	0.2317	36.063	-0.256	24.748
7	2.3634	-0.2669	-0.0599	1.8359	0.5514	4.1721	0.0847	0.1565	0.0984	0.0157	0.0121	-0.1928	0.1838	0.3562	-0.0993	0.2211	-0.0018	0.0045	0.2797	0.0438	0.314	43.121	6.659	39.992
8	0.536	0.5308	-1.0309	0.8982	0.4117	4.0939	0.0478	-0.0292	0.0023	0.0789	-0.0421	0.1653	-0.1673	-0.2788	0.0133	0.2416	0.072	-0.0083	0.3227	0.0599	0.3095	31.839	-13.162	68.517
9	2.9178	-1.1748	1.3329	2.9355	0.5903	1.4805	-0.1566	-0.5823	-0.9198	0.6393	0.2024	-0.4054	1.6639	0.274	-0.0497	0.9527	0.134	0.0705	0.4371	0.1664	0.7279	34.835	-37.595	83.507
10	2.1167	1.5978	-0.149	1.2107	-0.5742	2.7016	-0.1202	-0.1746	-0.3831	0.1718	0.021	0.0828	0.9546	-0.4461	0.1042	0.5037	-0.0482	0.0164	0.3421	0.074	0.412	29.817	-28.918	72.876
11	2.3863	0.3891	0.7977	2.1455	0.6285	4.5669	-0.0189	0.0638	-0.4072	-0.1592	0.0941	0.0495	0.3886	-0.0309	-0.0486	0.2652	-0.0053	-0.0064	0.2006	-0.0241	0.2433	36.489	-22.582	57.53
12	1.8144	-0.5779	0.3769	2.0834	1.1412	4.234	0.1056	-0.1987	-0.161	-0.102	-0.0077	0.0249	-0.2659	-0.3551	-0.0108	0.2831	0.0145	-0.0085	0.2302	0.039	0.2522	34.577	-13.45	64.391
13	2.7793	-1.1049	0.1019	4.2598	0.1665	4.5618	-0.1912	-0.2742	0.2398	0.1004	0.2312	-0.354	-0.6739	0.294	-0.1662	0.3344	-0.0021	0.061	0.3062	-0.028	0.2477	39.504	-4.406	74.829
14	2.6142	1.9309	1.3476	2.9355	-0.6522	2.6174	-0.0691	-0.2221	-0.2656	0.7517	0.1847	-0.0852	1.0679	0.5945	-0.2982	0.4261	0.166	-0.0524	0.5325	0.0592	0.3357	45.013	-20.254	87.436
15	2.4866	0.1529	-0.2472	3.8756	0.3775	4.4648	0.0627	-0.5161	-0.2237	0.4117	0.0504	0.118	0.3663	-0.0725	-0.0652	0.3246	0.0218	0.021	0.3591	0.0457	0.1971	35.422	-16.496	87.459

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN B AND RESID 36:71 )	B	36 - 71
2	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 72:93 )	B	72 - 93
3	X-RAY DIFFRACTION	3	( CHAIN B AND RESID 94:150 )	B	94 - 150
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 151:196 )	B	151 - 196
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 197:266 )	B	197 - 266
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 267:291 )	B	267 - 291
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 292:369 )	B	292 - 369
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 36:71 )	A	36 - 71
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 72:93 )	A	72 - 93
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 94:150 )	A	94 - 150
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 151:196 )	A	151 - 196
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 197:266 )	A	197 - 266
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 267:291 )	A	267 - 291
14	X-RAY DIFFRACTION	14	( CHAIN A AND RESID 292:311 )	A	292 - 311
15	X-RAY DIFFRACTION	15	( CHAIN A AND RESID 312:369 )	A	312 - 369

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