PDB-4tuf: Catalytic domain of the major endoglucanase from Xanthomonas camp...

ID or keywords:

Entry

Database: PDB / ID: 4tuf

Title

Catalytic domain of the major endoglucanase from Xanthomonas campestris pv. campestris

Components

Major extracellular endoglucanase

Keywords

HYDROLASE / Endoglucanase TIM barrel folding

Function / homology

Function and homology information

cellulase / polysaccharide binding / cellulase activity / cellulose catabolic process
Similarity search - Function

Biological species

Xanthomonas campestris pv. campestris (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.7 Å

Authors

Puhl, A.C. / Rosseto, F.R. / Polikarpov, I.

Citation

Journal: To Be Published
Title: Substrate cleavage pattern, biophysical characterization and crystallographic structure of the major endoglucanase from Xanthomonas campestris pv. campestris
Authors: Puhl, A.C. / Rosseto, F.R. / Stankovic, I. / Alvarez, T.M. / Squina, F.M. / Skaf, M.S. / Polikarpov, I.

History

Deposition	Jun 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0	Sep 27, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tuf.cif.gz	556.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4tuf.ent.gz	464.3 KB	Display	PDB format
PDBx/mmJSON format	4tuf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4tuf_validation.pdf.gz	471.4 KB	Display	wwPDB validaton report
Full document	4tuf_full_validation.pdf.gz	486.2 KB	Display
Data in XML	4tuf_validation.xml.gz	50.4 KB	Display
Data in CIF	4tuf_validation.cif.gz	70 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tu/4tuf ftp://data.pdbj.org/pub/pdb/validation_reports/tu/4tuf	HTTPS FTP

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Related structure data

Related structure data	2zumS S: Starting model for refinement
Similar structure data	5oxu-d 5oy1-d 5oy2-d 6pb9-d 5d1b-1 6oh6-d 6odc-3 6oda-3 5suw-d 6ekw-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2zumS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Major extracellular endoglucanase

B: Major extracellular endoglucanase

C: Major extracellular endoglucanase

D: Major extracellular endoglucanase

hetero molecules

156 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Major extracellular endoglucanase

hetero molecules

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

2

B: Major extracellular endoglucanase

hetero molecules

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

3

C: Major extracellular endoglucanase

hetero molecules

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

4

D: Major extracellular endoglucanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	174.660, 141.531, 108.008
Angle α, β, γ (deg.)	90.00, 110.49, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Major extracellular endoglucanase / Cellulase / Endo-1 / 4-beta-glucanase Mass: 38413.172 Da / Num. of mol.: 4 / Fragment: UNP residues 26-371 / Source method: isolated from a natural source Source: (natural) Xanthomonas campestris pv. campestris (bacteria) Strain: ATCC 33913 / NCPPB 528 / LMG 568 / References: UniProt: P19487, cellulase
#2: Chemical	... ChemComp-2HP / DIHYDROGENPHOSPHATE ION Mass: 96.987 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: H₂O₄P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.07 Å³/Da / Density % sol: 69.77 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris HCl pH 8.5, 2.0 M ammonium dihydrogen phosphate.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 24, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.7→107.039 Å / Num. obs: 67461 / % possible obs: 100 % / Redundancy: 3.6 % / B_iso Wilson estimate: 47.15 Å² / R_sym value: 0.096 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.619 / Mean I/σ(I) obs: 1.3 / R_sym value: 0.619 / % possible all: 100

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.4_1496)	refinement
SCALA	3.3.21	data scaling
XDS		data reduction
PDB_EXTRACT	3.14	data extraction
PHASER		phasing
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZUM

2zum

Resolution: 2.7→43.72 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.204	3412	5.06 %
R_work	0.165	-	-
obs	0.167	67446	100 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 56.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→43.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10776	0	135	241	11152

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11255
X-RAY DIFFRACTION	f_angle_d	0.811	15373
X-RAY DIFFRACTION	f_dihedral_angle_d	11.705	3870
X-RAY DIFFRACTION	f_chiral_restr	0.032	1609
X-RAY DIFFRACTION	f_plane_restr	0.004	1982

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 (%)
2.7-2.7386	0.2917	139	0.238	2641	X-RAY DIFFRACTION	100
2.7386-2.7794	0.2962	147	0.2345	2659	X-RAY DIFFRACTION	100
2.7794-2.8229	0.2706	119	0.2303	2683	X-RAY DIFFRACTION	100
2.8229-2.8691	0.236	127	0.2152	2679	X-RAY DIFFRACTION	100
2.8691-2.9186	0.3062	134	0.2446	2641	X-RAY DIFFRACTION	100
2.9186-2.9717	0.319	123	0.228	2692	X-RAY DIFFRACTION	100
2.9717-3.0288	0.2436	134	0.2193	2680	X-RAY DIFFRACTION	100
3.0288-3.0906	0.3185	136	0.205	2664	X-RAY DIFFRACTION	100
3.0906-3.1578	0.2361	139	0.2045	2651	X-RAY DIFFRACTION	100
3.1578-3.2312	0.2391	143	0.1935	2664	X-RAY DIFFRACTION	100
3.2312-3.312	0.268	145	0.1893	2661	X-RAY DIFFRACTION	100
3.312-3.4015	0.2144	151	0.202	2660	X-RAY DIFFRACTION	100
3.4015-3.5016	0.2504	131	0.1794	2685	X-RAY DIFFRACTION	100
3.5016-3.6145	0.1981	155	0.1599	2628	X-RAY DIFFRACTION	100
3.6145-3.7437	0.1881	157	0.1488	2650	X-RAY DIFFRACTION	100
3.7437-3.8935	0.1938	148	0.1447	2650	X-RAY DIFFRACTION	100
3.8935-4.0705	0.1742	148	0.1385	2641	X-RAY DIFFRACTION	100
4.0705-4.285	0.1568	151	0.129	2695	X-RAY DIFFRACTION	100
4.285-4.5532	0.1672	135	0.1187	2652	X-RAY DIFFRACTION	100
4.5532-4.9043	0.1464	163	0.1172	2700	X-RAY DIFFRACTION	100
4.9043-5.397	0.1482	154	0.1241	2648	X-RAY DIFFRACTION	100
5.397-6.1761	0.1882	150	0.1518	2668	X-RAY DIFFRACTION	100
6.1761-7.7742	0.2066	139	0.1695	2705	X-RAY DIFFRACTION	100
7.7742-43.7262	0.2014	144	0.1718	2737	X-RAY DIFFRACTION	100

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	8.0577	-0.4775	-2.7503	5.5352	4.7704	8.5559	-0.1479	0.7234	-0.6733	-0.4949	-0.0077	-0.6667	-0.058	0.1628	0.1077	0.2241	-0.0568	0.0412	0.3256	0.0324	0.5082	35.6593	-15.0201	-12.5682
2	2.5795	0.9347	-0.179	3.6667	-0.5329	1.5744	-0.2539	0.2329	0.7155	-0.0594	0.219	-0.0984	-0.3921	0.0986	0.0073	0.3956	-0.0875	-0.096	0.2966	0.0743	0.4901	26.0865	5.7854	-6.4985
3	6.6335	2.5305	-4.4525	2.7118	-2.604	5.5115	-0.1636	0.3662	0.4615	-0.0605	0.272	0.005	-0.2294	-0.2395	-0.1105	0.2503	-0.0455	-0.0787	0.1895	0.0173	0.3099	15.9151	-7.4769	-5.3746
4	1.534	0.5458	-0.2806	1.4092	0.6042	6.3729	-0.3171	0.015	-0.0621	-0.0559	0.0543	-0.084	0.3106	0.2894	0.2468	0.2166	-0.0064	0.011	0.1746	0.013	0.3697	21.0936	-19.6333	0.7658
5	2.6427	0.7863	-1.1185	5.2445	3.3283	6.7794	0.0065	-0.4472	-0.4132	0.6273	-0.0726	-0.6864	0.3439	0.373	0.0376	0.3526	0.0103	-0.0819	0.3244	0.1341	0.5204	35.7967	-17.3553	11.9602
6	2.8004	0.5376	1.2161	4.281	-3.2554	4.5235	0.1026	-0.4559	0.0738	0.3359	-0.0582	-0.5918	-0.4926	0.3123	-0.0642	0.2748	-0.0403	-0.0755	0.4063	0.0129	0.6329	38.5189	-7.5088	6.4606
7	7.6617	-5.3618	-0.2525	7.2317	0.1022	1.5102	-0.288	-0.3062	0.4502	0.4668	0.0768	-0.9098	0.0069	0.0675	0.0958	0.3361	-0.1644	-0.0941	0.4315	0.0934	0.6346	42.6766	1.4826	2.5514
8	1.5282	0.1661	-0.4152	2.6612	0.8461	2.642	0.1296	-0.5765	0.2049	0.2741	-0.0721	-0.0981	-0.5573	-0.0003	-0.0804	0.6386	0.0381	-0.1286	0.4892	-0.167	0.3529	11.696	-2.9642	37.9004
9	4.7841	-0.04	-0.3086	1.5511	0.1832	3.0502	0.1515	-0.5935	0.3255	0.2458	-0.1208	-0.3304	-0.0622	0.1528	-0.0069	0.5595	0.0021	-0.1522	0.4494	-0.1136	0.3337	20.3353	-10.2361	40.0079
10	1.3133	-0.2048	-0.3435	2.6287	1.9891	5.2382	-0.1504	-0.4111	0.0764	0.4401	0.1028	-0.0659	0.4429	0.1127	0.0553	0.2655	0.0403	-0.0223	0.3122	-0.0144	0.238	10.0757	-16.1784	28.4821
11	1.8158	0.4759	-0.695	2.0544	-1.3774	6.3179	-0.0266	-0.2242	0.2761	0.0771	0.0142	0.2205	-0.3031	-0.3397	-0.0121	0.224	0.0593	-0.069	0.2709	-0.0714	0.2878	0.4582	-9.2437	20.0072
12	7.599	3.0199	-2.345	5.0614	-1.1638	5.2167	-0.427	0.6495	0.7778	-0.4536	0.2166	0.0333	-1.1058	-0.1871	0.1339	0.705	0.0471	-0.2277	0.3593	-0.0916	0.5409	4.1041	8.8651	17.5287
13	6.7332	-2.5683	0.8651	5.5276	1.0546	5.8101	-0.3311	-0.1412	1.0021	0.5286	0.1395	-0.742	-1.1587	-0.0304	0.1698	0.5782	0.1371	-0.1283	0.3784	-0.123	0.5002	6.6089	7.0944	26.1213
14	2.4479	1.1794	2.4766	2.5739	-0.6084	4.5677	-0.2262	-0.4075	0.6927	0.0623	-0.0478	0.0573	-0.8637	0.2734	0.1648	0.8209	0.0851	-0.1866	0.515	-0.2532	0.5739	7.0861	10.1138	28.088
15	2.8037	-0.9372	2.9087	2.5422	-2.032	3.5476	0.0438	0.0699	0.3007	-0.2044	-0.0932	-0.1437	-0.7415	0.3551	0.0414	0.9237	-0.0451	-0.1277	0.6248	-0.2918	0.5534	16.6536	10.6079	34.3062
16	4.0197	-1.8786	-0.4439	3.4158	1.6092	2.2893	-0.0291	0.0269	0.0016	0.1049	0.0379	-0.1351	0.2244	0.3032	-0.0001	0.2722	0.065	-0.0085	0.2827	0.0622	0.4926	33.6618	-50.4704	6.912
17	2.0942	-1.0543	-1.1017	2.2097	0.7593	2.0385	0.0633	0.1617	-0.3169	-0.0185	-0.1577	0.1844	0.0191	-0.2252	0.0792	0.2376	0.0583	-0.0401	0.2805	0.0115	0.4929	19.3058	-46.2096	7.865
18	3.4588	0.5154	-0.3711	4.9194	0.8765	3.0472	-0.1008	-0.4643	-0.7483	0.6367	-0.0813	0.3773	0.8027	-0.243	0.1818	0.563	0.0018	0.0693	0.4026	-0.0201	0.9085	16.4188	-66.2812	13.2163
19	7.6646	1.09	1.3863	2.4246	-0.6728	0.8771	-0.0869	-0.23	-0.4051	0.3914	-0.079	0.5831	0.5292	-0.0033	0.1571	0.483	0.1103	0.0955	0.3346	-0.0743	0.7691	29.4001	-66.3785	10.9647
20	2.0232	-0.2573	0.7392	3.4747	0.0139	1.599	0.1333	-0.181	-0.0666	-0.3457	-0.1511	0.0889	0.028	-0.1413	0.0317	0.9235	0.1125	-0.1503	0.6224	0.172	0.4593	12.3314	-50.1647	50.0379
21	1.2057	-0.5216	1.1872	2.8913	-1.2601	2.0808	0.0998	-0.2216	-0.4164	0.1038	0.0657	-0.1426	0.864	-0.2392	-0.1745	0.9348	0.1	-0.0765	0.6463	0.2243	0.5666	12.8392	-63.0336	47.5575
22	2.0733	-1.364	1.9793	6.6404	-4.9302	3.9514	0.0712	-0.2587	-0.3025	0.3394	-0.0438	-0.5055	0.5869	-0.228	-0.0033	0.5434	0.015	-0.0528	0.4543	0.1092	0.5528	7.9793	-54.3505	40.8544
23	4.3298	-2.068	5.3111	3.9865	-2.3242	7.7441	0.1131	-0.4133	-0.3894	0.439	-0.087	-0.0984	0.7996	-0.8218	-0.024	0.7199	0.0299	0.051	0.4938	0.1049	0.3901	1.5678	-50.2974	41.4881
24	1.8402	0.9357	-1.5852	2.3167	0.1031	2.1226	-0.2975	-0.5313	-0.3243	0.1652	-0.0046	-0.2128	0.0238	0.1732	0.2999	0.5197	0.1488	-0.0358	0.4774	0.1706	0.4299	11.1687	-37.5456	35.5236
25	0.8284	0.1295	0.559	2.1753	2.3354	2.7389	-0.0973	0.1379	0.2751	-0.25	0.0671	-0.4516	-0.2592	0.2599	0.0211	0.717	0.0528	-0.1931	0.6917	0.2119	0.7397	27.4428	-31.0716	39.6969
26	5.3936	-3.6026	0.3815	6.4115	0.8412	3.695	0.762	-0.0114	-0.4472	0.0461	-0.5286	-0.6372	0.6108	0.8475	-0.1769	0.6787	0.224	-0.1637	0.701	0.1128	0.6815	23.032	-41.3387	44.8708
27	1.8492	-0.7307	0.3132	7.8472	-4.0296	2.2459	-0.2638	-0.0405	-0.2301	0.4428	0.2644	-0.6143	0.4035	0.5992	0.0366	0.8976	0.0795	-0.2932	0.6885	0.0851	0.731	25.9737	-43.0265	46.6222
28	1.6428	0.2111	0.4898	9.9131	3.5511	1.5686	0.2104	-0.3235	-0.2736	0.2003	-0.2695	-1.0048	-0.2351	-0.5543	0.0526	1.1182	0.0958	-0.2681	0.7417	0.3042	0.7498	28.1881	-51.7508	52.6374

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 26 THROUGH 48 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 49 THROUGH 137 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 138 THROUGH 178 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 179 THROUGH 258 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 259 THROUGH 298 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 299 THROUGH 346 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 347 THROUGH 371 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 26 THROUGH 91 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 92 THROUGH 137 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 138 THROUGH 178 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 179 THROUGH 255 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 256 THROUGH 293 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 294 THROUGH 313 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 314 THROUGH 341 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 342 THROUGH 371 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 26 THROUGH 105 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 106 THROUGH 255 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 256 THROUGH 312 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 313 THROUGH 371 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 26 THROUGH 66 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 67 THROUGH 112 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 113 THROUGH 153 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 154 THROUGH 183 )
24	X-RAY DIFFRACTION	24	CHAIN 'D' AND (RESID 184 THROUGH 273 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 274 THROUGH 293 )
26	X-RAY DIFFRACTION	26	CHAIN 'D' AND (RESID 294 THROUGH 312 )
27	X-RAY DIFFRACTION	27	CHAIN 'D' AND (RESID 313 THROUGH 346 )
28	X-RAY DIFFRACTION	28	CHAIN 'D' AND (RESID 347 THROUGH 371 )

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