PDB-2ylk: Carbohydrate-binding module CBM3b from the cellulosomal cellobioh...

ID or keywords:

Entry

Database: PDB / ID: 2ylk

Title

Carbohydrate-binding module CBM3b from the cellulosomal cellobiohydrolase 9A from Clostridium thermocellum

Components

CELLULOSE 1,4-BETA-CELLOBIOSIDASE

Keywords

HYDROLASE / CELLULOSE BINDING PROTEIN

Function / homology

Function and homology information

Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function

Biological species

CLOSTRIDIUM THERMOCELLUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Yaniv, O. / Petkun, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: A Single Mutation Reforms the Binding Activity of an Adhesion-Deficient Family 3 Carbohydrate-Binding Module
Authors: Yaniv, O. / Petkun, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.

History

Deposition	Jun 2, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 27, 2012	Group: Other
Revision 1.2	Jul 11, 2012	Group: Other
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2ylk.cif.gz	247 KB	Display	PDBx/mmCIF format
PDB format	pdb2ylk.ent.gz	201.7 KB	Display	PDB format
PDBx/mmJSON format	2ylk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2ylk_validation.pdf.gz	446.8 KB	Display	wwPDB validaton report
Full document	2ylk_full_validation.pdf.gz	452.9 KB	Display
Data in XML	2ylk_validation.xml.gz	25.1 KB	Display
Data in CIF	2ylk_validation.cif.gz	35.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yl/2ylk ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2ylk	HTTPS FTP

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Related structure data

Related structure data	3zqxC 2wnxS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4c8x-1 3j6l-d 1od9-d 1ol0-2 4ahh-d 4jnj-1 3zqx-d 6my0-2 6ck8-2 6ck8-1 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

3zqxC

2wnxS

C: citing same article (ref.)

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	#74 - Feb 2006 alpha-Amylase similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

B: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

C: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

D: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

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

1

A: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

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

2

B: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

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

3

C: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

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

4

D: CELLULOSE 1,4-BETA-CELLOBIOSIDASE

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

Unit cell

Length a, b, c (Å)	95.456, 95.456, 82.911
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

#1: Protein	CELLULOSE 1,4-BETA-CELLOBIOSIDASE Mass: 16561.348 Da / Num. of mol.: 4 Fragment: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 1004-1147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL References: UniProt: Q59325, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

CELLULOSE 1,4-BETA-CELLOBIOSIDASE

Mass: 16561.348 Da / Num. of mol.: 4
Fragment: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 1004-1147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL
References: UniProt: Q59325, cellulose 1,4-beta-cellobiosidase (non-reducing end)

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.71 Å³/Da / Density % sol: 54.7 % / Description: NONE
Crystal grow	pH: 7.5 Details: 20%(V/V) PEG 3350 0.2 M DIAMMONIUM HYDROGEN CITRATE., pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97
Detector	Type: ADSC CCD / Detector: CCD / Date: Dec 12, 2010 / Details: MIRRORS
Radiation	Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 37875 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.97 % / B_iso Wilson estimate: 34.16 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 17.3
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WNX

2wnx

Resolution: 2.2→42.689 Å / SU ML: 0.7 / σ(F): 1.35 / Phase error: 23.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2261	1870	5 %
R_work	0.1727	-	-
obs	0.1753	37377	98.67 %

Solvent computation

Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.365 Å² / k_sol: 0.347 e/Å³

Displacement parameters

B_iso mean: 38.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7397 Å²	0 Å²	0 Å²
2-	-	0.7397 Å²	0 Å²
3-	-	-	-1.4793 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→42.689 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4652	0	0	288	4940

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4892
X-RAY DIFFRACTION	f_angle_d	1.228	6458
X-RAY DIFFRACTION	f_dihedral_angle_d	15.896	1736
X-RAY DIFFRACTION	f_chiral_restr	0.089	665
X-RAY DIFFRACTION	f_plane_restr	0.005	849

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 (%)
2.2-2.2595	0.3317	140	0.2651	2755	X-RAY DIFFRACTION	100
2.2595-2.326	0.3192	138	0.2454	2754	X-RAY DIFFRACTION	100
2.326-2.401	0.2815	152	0.2337	2745	X-RAY DIFFRACTION	100
2.401-2.4868	0.3394	143	0.2289	2753	X-RAY DIFFRACTION	100
2.4868-2.5864	0.2751	142	0.2178	2765	X-RAY DIFFRACTION	100
2.5864-2.7041	0.2823	158	0.2012	2729	X-RAY DIFFRACTION	100
2.7041-2.8466	0.2533	138	0.1845	2764	X-RAY DIFFRACTION	100
2.8466-3.0249	0.2359	159	0.1798	2726	X-RAY DIFFRACTION	100
3.0249-3.2584	0.2184	155	0.1597	2718	X-RAY DIFFRACTION	99
3.2584-3.5862	0.2005	150	0.1509	2758	X-RAY DIFFRACTION	99
3.5862-4.1047	0.1979	140	0.1439	2692	X-RAY DIFFRACTION	97
4.1047-5.1701	0.1501	125	0.1214	2684	X-RAY DIFFRACTION	96
5.1701-42.6972	0.213	130	0.1835	2664	X-RAY DIFFRACTION	93

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	1.7485	1.318	-0.9251	1.6401	-0.0524	5.9098	0.1439	0.0135	-0.0233	0.2875	0.1358	0.2612	0.1445	-0.4213	-0.1664	0.1703	0.0513	-0.0042	0.1396	0.0382	0.1738	-13.1017	7.1781	-11.74
2	2.7162	0.3449	-1.3918	2.4948	1.3475	1.7286	-0.0636	0.3753	0.0229	-0.3808	0.1464	0.1686	-0.2842	-0.0275	-0.0764	0.1876	0.0065	-0.0175	0.2067	0.0111	0.1753	-9.1224	16.3134	-24.086
3	2.1499	0.1126	-1.4261	2.2812	-1.774	5.5817	0.2574	0.1349	0.1436	0.401	0.2324	0.3798	-0.824	-0.4858	-0.3926	0.1595	0.0445	0.0008	0.2479	0.0192	0.2782	-19.7552	17.9218	-10.4536
4	2.4637	-0.0188	-1.1038	1.4091	-0.699	1.7994	0.0611	-0.5932	-0.086	0.375	0.0217	-0.0946	-0.4333	0.3337	0.0013	0.2148	-0.0119	0.0176	0.2808	0.0105	0.1414	-8.6738	19.9063	-9.3793
5	1.3756	-0.3179	-1.2243	1.1559	-0.1913	3.5788	0.2541	-0.0888	0.1561	0.0347	0.0049	0.1035	-0.5088	0.0979	-0.1384	0.1751	0.0329	0.0479	0.1727	0.0091	0.2237	-12.8551	18.2018	-14.4862
6	0.8547	-0.229	-0.1418	1.8615	0.1377	2.7658	0.0101	0.0984	0.1265	0.0502	0.0401	0.1588	0.472	-0.2741	-0.04	0.1405	0.0044	-0.0136	0.1602	0.0461	0.2315	-17.4369	6.1163	-9.9653
7	5.0715	-0.3741	0.3379	5.4882	0.9846	4.6353	-0.0038	0.5884	0.1705	0.0705	0.0753	0.2889	-0.795	-0.4469	-0.0209	0.2404	0.0983	0.0103	0.2905	-0.0134	0.1865	-21.3415	16.8321	-23.2008
8	1.2369	0.3556	1.2148	1.947	1.1133	3.7865	-0.0472	0.0425	-0.0761	0.079	0.0992	-0.1631	-0.26	0.367	0.0488	0.1383	0.0206	0.0356	0.2016	0.0317	0.1891	-34.5432	40.9156	-7.8137
9	3.7488	1.0493	1.3647	1.5179	0.0497	2.4122	-0.006	0.3561	-0.2529	-0.414	0.1611	-0.1246	0.1249	0.3372	-0.2008	0.3159	0.0305	0.12	0.2638	-0.0102	0.3042	-31.4199	29.5545	-18.8328
10	2.3235	0.6113	-0.2576	1.9969	-1.0178	9.4803	0.0913	0.1961	-0.8466	0.9844	-0.0188	-1.2646	0.2811	1.2688	0.0552	0.2213	0.0311	0.0198	0.3871	0.0524	0.3964	-21.4867	36.5772	4.6121
11	1.3535	-0.1881	0.7233	1.6361	0.5086	2.0898	0.0117	-0.2049	-0.1679	0.0215	-0.1111	-0.0987	0.1763	0.1662	0.0703	0.1402	0.0557	0.0495	0.2454	0.0463	0.2534	-33.3673	30.9984	-7.0343
12	1.3335	0.2033	-0.3033	1.7262	-0.039	3.138	-0.0237	0.1168	-0.171	0.0079	-0.06	-0.1689	-0.3369	0.5152	0.0512	0.161	0.0229	0.0303	0.2009	0.0402	0.24	-29.519	44.5817	-4.2504
13	3.8192	-1.3659	-0.8621	5.7932	0.0173	3.7181	-0.0559	-0.1451	-0.2633	-0.4925	0.0576	-0.4192	0.1833	0.3742	-0.0488	0.2825	0.0728	0.0562	0.2597	0.0484	0.2123	-23.8982	34.8095	-17.6198
14	2.5514	-0.0136	0.4228	0.4256	1.0245	4.9211	-0.1019	-0.0605	-0.0787	-0.0959	-0.114	-0.097	-0.2642	-0.2682	0.205	0.2253	-0.0121	0.0213	0.1753	0.0222	0.2539	-52.0517	33.1988	12.3248
15	2.0768	-0.314	0.1697	1.0081	0.9095	1.4082	-0.0347	-0.2026	-0.2303	0.2472	0.0389	0.0495	0.4331	0.0057	0.0166	0.2863	0.03	0.0212	0.2193	0.0721	0.2302	-43.5684	26.3663	22.5209
16	2.3614	0.1068	0.8335	2.2881	0.2228	3.0194	-0.2118	0.5336	-0.0755	-0.1416	0.3151	0.0566	0.2309	0.3911	0.0154	0.2221	-0.0351	0.0165	0.217	0.0659	0.1924	-44.4061	24.9129	7.2289
17	1.718	-0.5793	2.4054	1.1434	0.2465	4.3326	0.1239	0.0239	-0.2239	0.1139	-0.0463	0.0749	0.4927	0.2108	-0.0232	0.2758	-0.0163	0.0451	0.2296	0.0168	0.2496	-44.0543	25.4005	15.2085
18	1.1906	0.2802	0.5338	0.926	-0.2484	1.9232	0.0674	-0.1309	0.0364	0.0613	-0.1098	0.0933	0.0782	-0.4727	-0.0005	0.2075	0.0141	0.0547	0.2531	0.0327	0.2395	-55.8942	30.8419	10.6461
19	4.7935	-0.0927	0.5048	4.0449	-0.08	4.8303	-0.0717	-0.4048	-1.0487	-0.3739	-0.0266	-0.0821	0.8935	-0.0763	-0.0366	0.413	-0.055	0.0486	0.3042	0.1181	0.3419	-50.9607	20.5287	23.8053
20	2.4978	0.0819	0.0292	1.0202	-1.3299	2.5903	0.0186	-0.4274	0.1359	0.2914	-0.0379	0.0677	-0.1127	0.1177	0.0644	0.3093	-0.0604	0.0059	0.235	-0.0564	0.2044	2.5956	18.4703	12.5313
21	7.5955	-0.4753	0.3273	6.4978	-0.8837	8.0533	0.0925	1.0579	0.1211	-0.6868	-0.6605	-0.3946	-1.4667	1.1104	0.4826	0.376	-0.008	-0.0306	0.3583	-0.0067	0.2867	11.0649	26.0869	-4.4561
22	1.546	0.3385	-1.8584	1.6434	-0.3962	2.8519	-0.0881	-0.0277	-0.061	0.0153	0.0282	0.02	-0.1899	-0.1617	0.0646	0.2831	-0.0474	0.0088	0.2773	-0.0394	0.235	-1.8979	22.8605	8.5901
23	1.4294	0.1289	-0.2727	0.5003	-0.3924	3.2762	0.1152	-0.2265	0.1391	0.1403	-0.0955	-0.0929	-0.2329	0.3005	-0.017	0.2527	-0.0528	-0.001	0.2572	-0.0648	0.2434	8.5661	19.3394	8.4059

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN C AND (RESSEQ 1:17)
2	X-RAY DIFFRACTION	2	CHAIN C AND (RESSEQ 18:33)
3	X-RAY DIFFRACTION	3	CHAIN C AND (RESSEQ 34:50)
4	X-RAY DIFFRACTION	4	CHAIN C AND (RESSEQ 51:70)
5	X-RAY DIFFRACTION	5	CHAIN C AND (RESSEQ 71:102)
6	X-RAY DIFFRACTION	6	CHAIN C AND (RESSEQ 103:127)
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESSEQ 128:145)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 1:26)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 27:42)
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESSEQ 43:50)
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESSEQ 51:102)
12	X-RAY DIFFRACTION	12	CHAIN A AND (RESSEQ 103:127)
13	X-RAY DIFFRACTION	13	CHAIN A AND (RESSEQ 128:145)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 1:17)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 18:42)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESSEQ 43:70)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESSEQ 71:102)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESSEQ 103:127)
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESSEQ 128:145)
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESSEQ 1:42)
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESSEQ 43:50)
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 51:95)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 96:145)

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