PDB-4ba6: High Resolution structure of the C-terminal family 65 Carbohydrat...

ID or keywords:

Entry

Database: PDB / ID: 4ba6

Title

High Resolution structure of the C-terminal family 65 Carbohydrate Binding Module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens

Components

Endoglucanase cel5A

Keywords

CARBOHYDRATE-BINDING PROTEIN / PLANT CELL WALL DEGRADATION / BETA-JELLY ROLL

Function / homology

Function and homology information

organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function

Biological species

Eubacterium cellulosolvens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.42 Å

Authors

Venditto, I. / Luis, A.S. / Basle, A. / Temple, M. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Gilbert, H.J. / Najmudin, S.

Citation

Journal: J. Biol. Chem. / Year: 2013
Title: Understanding how noncatalytic carbohydrate binding modules can display specificity for xyloglucan.
Authors: Luis, A.S. / Venditto, I. / Temple, M.J. / Rogowski, A. / Basle, A. / Xue, J. / Knox, J.P. / Prates, J.A. / Ferreira, L.M. / Fontes, C.M. / Najmudin, S. / Gilbert, H.J.

History

Deposition	Sep 11, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 30, 2013	Group: Database references
Revision 1.2	Feb 27, 2013	Group: Database references
Revision 1.3	Mar 20, 2013	Group: Database references
Revision 1.4	Dec 5, 2018	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq_dif Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_ec / _entity.src_method / _pdbx_struct_mod_residue.details / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.5	May 8, 2019	Group: Data collection / Derived calculations / Experimental preparation Category: exptl_crystal_grow / struct_conn Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ba6.cif.gz	74.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ba6.ent.gz	56.1 KB	Display	PDB format
PDBx/mmJSON format	4ba6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ba/4ba6 ftp://data.pdbj.org/pub/pdb/validation_reports/ba/4ba6	HTTPS FTP

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Related structure data

Related structure data	2ypjC 4aekC 4aemC 4afdC 4afmSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6mor-d 7aa0-1 6bth-2 2cbs-d 7jz5-1 2qfd-1 2fs6-2 1bm5-d 1ebt-d 7aa0-2 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Endoglucanase cel5A

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	83.570, 83.570, 36.750
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Endoglucanase cel5A Mass: 15973.568 Da / Num. of mol.: 1 Fragment: C-TERMINAL FAMILY 65 CARBOHYDRATE BINDING MODULE (CBM65B), RESIDUES 581-713 Source method: isolated from a genetically manipulated source Details: METHIONINE 620 (MET A620) HAS BEEN OXIDISED TO METHIONINE SULPHOXIDE (SME 620) Source: (gene. exp.) Eubacterium cellulosolvens (bacteria) / Gene: cel5A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q3LHN3
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	METHIONINE SULFOXIDE (SME): METHIONINE SULFOXIDE GLYCEROL (GOL): FROM THE CRYOPROTECTANT

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	Temperature: 292 K / pH: 7 / Details: 2M AMMONIUM SULPHATE, 292 K, pH 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.42→36.75 Å / Num. obs: 27755 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / R_merge(I) obs: 0.06 / Net I/σ(I): 11.9
Reflection shell	Resolution: 1.42→1.5 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AFM

4afm

Resolution: 1.42→72.37 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.966 / SU B: 2.826 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. RESIDUES 578-581, MASS AND 710-721 GSEDLEHHHHHH ARE DISORDERED. ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19728	1402	5.1 %	RANDOM
R_work	0.16982	-	-	-
obs	0.17121	26328	99.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 23.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.07 Å²	0.54 Å²	0 Å²
2-	-	1.07 Å²	0 Å²
3-	-	-	-1.61 Å²

Refinement step

Cycle: LAST / Resolution: 1.42→72.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	6	166	1173

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.02	1105
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.495	1.951	1523
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.463	5	150
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.966	25.962	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.207	15	175
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	0.81	15	1
X-RAY DIFFRACTION	r_chiral_restr	0.206	0.2	167
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	864
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.421→1.458 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	108	-
R_work	0.354	1835	-
obs	-	-	99.44 %

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	11.0525	-3.6221	5.7468	1.6607	-0.3168	8.203	-0.1646	0.0572	0.4613	-0.0278	-0.0228	-0.1404	-0.2922	0.1897	0.1875	0.0501	0.0245	-0.0021	0.1439	-0.0484	0.1211	26.078	40.4205	5.0707
2	1.761	1.6507	-0.8748	7.6158	-3.1396	9.7336	0.0321	0.0466	0.1227	-0.1025	-0.005	-0.2096	-0.1622	-0.0057	-0.0271	0.0424	0.0284	0.0202	0.0597	-0.0113	0.0509	33.0664	29.7591	11.7121
3	0.0812	0.0218	-0.41	0.39	1.7173	10.8821	-0.0034	0.0076	-0.0432	0.01	0.0178	-0.0627	0.1922	-0.0498	-0.0145	0.0823	0.0274	0.0038	0.0777	-0.0076	0.0298	31.1142	23.5316	26.8545
4	13.3462	4.8171	0.1673	10.1976	0.8805	5.0569	0.157	-0.6356	-0.4171	0.1546	0.2956	-1.0615	-0.0126	0.7123	-0.4526	0.0909	0.0513	0.006	0.1888	-0.0723	0.1413	33.0829	29.4798	39.1638
5	2.1996	0.2675	-3.7226	5.512	5.8047	22.6481	0.195	-0.3902	-0.3926	0.3063	0.294	-0.3598	0.7265	0.504	-0.489	0.1287	-0.0264	-0.0972	0.173	0.0993	0.1698	35.28	29.6181	30.9525
6	10.0235	6.2847	-4.4074	4.6469	-3.1092	2.1091	-0.1511	0.257	-0.1232	0.0085	0.1692	0.0804	0.0216	-0.1009	-0.0181	0.0499	0.0254	0.0128	0.1086	0.0009	0.045	39.9267	33.1159	20.3546
7	1.9556	0.7012	0.8701	10.2965	2.6006	5.1179	0.0255	0.2089	0.1323	-0.1134	-0.1097	0.6038	-0.0206	-0.2347	0.0843	0.0404	0.002	0	0.128	-0.0019	0.0618	45.6614	35.6772	16.7007
8	13.8824	-5.0899	-1.8235	21.3425	6.0087	9.7918	0.0946	0.6107	0.1995	-0.4402	0.0649	-0.1532	-0.1464	0.3118	-0.1595	0.0532	-0.0027	-0.0065	0.1582	0.0265	0.0116	37.0144	42.5057	10.444
9	0.0507	-0.4079	0.3774	5.2027	-0.9223	5.9697	-0.0009	0.0108	0.0112	-0.1339	-0.0267	0.0779	-0.2093	-0.0127	0.0276	0.0353	0.0327	-0.0121	0.0726	0.0363	0.096	29.3022	42.3309	13.35
10	1.2207	0.8526	0.314	2.3074	0.2854	2.2007	0.0059	0.025	-0.0137	-0.0788	0.0197	0.0425	0.1395	-0.2496	-0.0255	0.0541	0.0341	0.0026	0.0968	0.0025	0.074	24.6306	30.5845	22.6872
11	9.1342	2.6325	2.2593	2.6463	1.6347	2.296	-0.1122	-0.0627	0.2657	-0.0478	0.0327	-0.0233	-0.1263	0.1369	0.0795	0.0588	0.0168	-0.0183	0.0723	0.0073	0.06	37.3058	41.5972	24.3505
12	10.2906	-5.3932	0.0934	9.463	4.6622	7.1671	-0.0784	-0.8326	1.2885	-0.1752	0.382	-0.4082	-0.3491	0.5992	-0.3036	0.0512	-0.0369	-0.0159	0.2027	-0.1751	0.2574	43.9279	45.4435	29.0303
13	6.7238	0.5978	1.5489	0.3801	-0.198	1.1331	0.1042	-0.3627	0.1555	0.1041	-0.0645	0.008	-0.0416	-0.0758	-0.0397	0.0663	0.0279	-0.0116	0.0814	-0.0129	0.0237	30.5161	40.7233	27.7566
14	2.1169	0.2813	0.1422	7.7184	-1.0185	2.5189	-0.0533	0.1086	-0.0458	-0.1963	-0.0604	0.1539	0.0021	-0.2639	0.1138	0.0287	0.0303	-0.0073	0.095	-0.0042	0.0355	19.3834	35.8361	18.5072
15	3.1232	1.422	0.9834	3.5029	0.1271	5.0184	-0.0953	-0.071	0.3388	0.0621	-0.047	0.0309	-0.4469	0.0144	0.1423	0.0721	0.0352	-0.015	0.0466	-0.0021	0.0857	28.6304	46.0331	20.5982
16	5.4236	-6.5292	-4.2626	12.9244	-0.4431	9.5132	0.3393	0.3124	0.5303	-0.375	-0.2823	-0.8871	-0.3167	-0.3047	-0.057	0.1204	-0.0282	-0.1021	0.0408	0.0883	0.2384	37.2469	49.5167	20.4307
17	8.0197	3.8611	-0.574	4.2742	0.048	1.4131	-0.0585	0.1457	0.2324	0.0263	0.0655	-0.0193	-0.1696	0.1035	-0.007	0.062	0.0095	-0.0109	0.0776	0.009	0.0547	40.0366	39.1538	22.5174
18	5.0272	1.9847	0.047	4.1863	1.354	2.4906	0.0989	-0.1631	-0.1528	0.25	-0.1214	0.0379	0.0363	-0.0579	0.0224	0.0535	0.0457	0	0.0891	-0.003	0.0615	27.204	28.9865	32.6769
19	1.022	0.9473	-0.1022	2.678	-2.4426	6.617	0.0353	0.0212	-0.022	0.0252	0.0919	0.0785	0.0173	-0.278	-0.1271	0.0627	0.0352	0.0084	0.0806	-0.0036	0.0714	27.6486	27.1356	20.2884
20	18.4268	-6.6362	0.9522	3.0547	-3.1524	11.9849	0.1753	1.7365	-0.2154	0.387	-0.8705	-0.0496	-1.9193	1.2683	0.6952	0.3863	-0.1649	-0.2542	0.282	0.0225	0.3202	29.4327	44.0205	7.596

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	582 - 587
2	X-RAY DIFFRACTION	2	A	588 - 592
3	X-RAY DIFFRACTION	3	A	593 - 599
4	X-RAY DIFFRACTION	4	A	600 - 605
5	X-RAY DIFFRACTION	5	A	606 - 610
6	X-RAY DIFFRACTION	6	A	611 - 615
7	X-RAY DIFFRACTION	7	A	616 - 620
8	X-RAY DIFFRACTION	8	A	621 - 626
9	X-RAY DIFFRACTION	9	A	627 - 630
10	X-RAY DIFFRACTION	10	A	631 - 640
11	X-RAY DIFFRACTION	11	A	641 - 645
12	X-RAY DIFFRACTION	12	A	646 - 650
13	X-RAY DIFFRACTION	13	A	651 - 656
14	X-RAY DIFFRACTION	14	A	657 - 665
15	X-RAY DIFFRACTION	15	A	666 - 674
16	X-RAY DIFFRACTION	16	A	675 - 680
17	X-RAY DIFFRACTION	17	A	681 - 688
18	X-RAY DIFFRACTION	18	A	689 - 694
19	X-RAY DIFFRACTION	19	A	695 - 704
20	X-RAY DIFFRACTION	20	A	705 - 709

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