PDB-4c8x: Crystal structure of carbohydrate-binding module CBM3b mutant (Y5...

ID or keywords:

Entry

Database: PDB / ID: 4c8x

Title

Crystal structure of carbohydrate-binding module CBM3b mutant (Y56S) from the cellulosomal cellobiohydrolase 9A from Clostridium thermocellum

Components

CELLULOSE 1,4-BETA-CELLOBIOSIDASE

Keywords

HYDROLASE / CBM / CELLULOSOME / CBH9A

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: 1.998 Å

Authors

Yaniv, O. / Bayer, E.A. / Lamed, R. / Frolow, F.

Citation

Journal: To be Published
Title: Crystal Structure of Carbohydrate-Binding Module Cbm3B Mutant (Y56S) from the Cellulosomal Cellobiohydrolase 9A from Clostridium Thermocellum
Authors: Yaniv, O. / Bayer, E.A. / Lamed, R. / Frolow, F.

History

Deposition	Oct 2, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	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	4c8x.cif.gz	247.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4c8x.ent.gz	201.9 KB	Display	PDB format
PDBx/mmJSON format	4c8x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4c8x_validation.pdf.gz	433.4 KB	Display	wwPDB validaton report
Full document	4c8x_full_validation.pdf.gz	435.3 KB	Display
Data in XML	4c8x_validation.xml.gz	25.6 KB	Display
Data in CIF	4c8x_validation.cif.gz	37.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c8/4c8x ftp://data.pdbj.org/pub/pdb/validation_reports/c8/4c8x	HTTPS FTP

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Related structure data

Related structure data	2ylkS S: Starting model for refinement
Similar structure data	2ylk-3 2ylk-1 2ylk-2 6xx1-4 2ylk-4 6xx1-1 6f1d-d 3pof-2 3j6l-d 3poi-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

2ylkS

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

65.8 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
16.5 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
16.5 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
16.5 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
16.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.186, 95.186, 83.637
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 / CARBOHYDRATE-BINDING MODULE FAMILY 3B Mass: 16458.227 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 1004-1147 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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.: 403 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

CELLULOSE 1,4-BETA-CELLOBIOSIDASE / CARBOHYDRATE-BINDING MODULE FAMILY 3B

Mass: 16458.227 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 1004-1147 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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.: 403 / 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: 2.55 Å³/Da / Density % sol: 51.82 % / Description: NONE
Crystal grow	pH: 7.5 Details: 0.2M DIAMMONIUM HYDROGEN CITRATE, 20% PEG3350, pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9299
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2009 / Details: MIRRORS
Radiation	Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9299 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 50720 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.93 % / B_iso Wilson estimate: 26.01 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 13
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / % 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 2YLK

2ylk

Resolution: 1.998→47.593 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 21.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.203	2361	5.1 %
R_work	0.161	-	-
obs	0.1631	46648	92.01 %

Solvent computation

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

Displacement parameters

B_iso mean: 21.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.09 Å²	0 Å²	0 Å²
2-	-	-0.09 Å²	0 Å²
3-	-	-	0.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.998→47.593 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4620	0	0	403	5023

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4736
X-RAY DIFFRACTION	f_angle_d	1.063	6416
X-RAY DIFFRACTION	f_dihedral_angle_d	15.941	1720
X-RAY DIFFRACTION	f_chiral_restr	0.045	668
X-RAY DIFFRACTION	f_plane_restr	0.004	848

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 (%)
1.9975-2.0383	0.2657	84	0.208	1425	X-RAY DIFFRACTION	51
2.0383-2.0826	0.2488	100	0.2001	1811	X-RAY DIFFRACTION	64
2.0826-2.1311	0.3052	101	0.203	2120	X-RAY DIFFRACTION	76
2.1311-2.1844	0.2712	128	0.2083	2411	X-RAY DIFFRACTION	85
2.1844-2.2434	0.2573	145	0.2068	2604	X-RAY DIFFRACTION	93
2.2434-2.3094	0.2585	144	0.1922	2776	X-RAY DIFFRACTION	97
2.3094-2.384	0.2274	146	0.1977	2799	X-RAY DIFFRACTION	99
2.384-2.4692	0.2646	140	0.1907	2792	X-RAY DIFFRACTION	100
2.4692-2.568	0.2287	149	0.1787	2827	X-RAY DIFFRACTION	100
2.568-2.6849	0.2445	149	0.1714	2825	X-RAY DIFFRACTION	100
2.6849-2.8264	0.2131	143	0.1651	2845	X-RAY DIFFRACTION	100
2.8264-3.0035	0.2148	160	0.165	2820	X-RAY DIFFRACTION	100
3.0035-3.2353	0.1969	156	0.158	2816	X-RAY DIFFRACTION	100
3.2353-3.5608	0.1861	145	0.1491	2828	X-RAY DIFFRACTION	100
3.5608-4.0758	0.1831	162	0.1375	2841	X-RAY DIFFRACTION	100
4.0758-5.1342	0.1445	151	0.1187	2852	X-RAY DIFFRACTION	100
5.1342-47.6065	0.1772	158	0.1638	2895	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	1.9729	0.9402	-2.3324	1.2317	-1.2516	9.9517	-0.0482	-0.023	-0.0859	0.0176	-0.1197	-0.0054	-0.0216	0.1664	0.2047	0.1866	0.0424	-0.0053	0.1714	-0.0083	0.2011	-13.0029	7.1816	2.1771
2	4.2874	1.373	-3.1768	2.6858	0.5786	3.7922	-0.076	0.2337	0.2084	-0.4996	0.0963	0.0913	-0.0716	0.117	-0.0286	0.1579	0.0122	-0.001	0.1778	0.0166	0.1696	-9.0388	16.3413	-10.1425
3	3.5069	0.8415	-1.6864	1.9441	0.4945	3.7659	0.1271	0.2971	0.1054	0.118	0.0867	0.1892	-0.3504	-0.6077	-0.2112	0.1572	0.091	0.0114	0.1619	0.0665	0.2479	-19.6756	17.8445	3.6562
4	4.2765	-0.9148	-5.5999	1.2283	1.2162	7.3111	-0.3756	-0.4102	-0.137	0.1733	0.2856	-0.0798	0.1692	0.4464	0.0708	0.2043	0.0116	0.0095	0.2703	0.0266	0.219	-6.424	17.7562	5.1817
5	1.8152	-0.6207	-1.7542	1.502	-0.2875	4.7935	0.1176	-0.0234	0.1046	-0.025	0.0595	0.1018	-0.338	-0.0215	-0.1591	0.1604	0.0115	0.0163	0.1505	0.0163	0.1882	-12.6219	19.1823	0.3452
6	1.0414	-0.0646	0.1328	1.5713	0.6629	3.3897	0.0564	0.0772	-0.1394	-0.0263	0.0023	0.0457	0.223	-0.2239	-0.0429	0.1685	0.0047	0.0168	0.195	0.0347	0.2183	-17.7754	8.1466	1.7626
7	6.2559	2.0651	-2.506	6.3439	1.0355	6.6982	0.0775	0.3948	0.5011	-0.6058	0.2336	0.5169	-0.3357	-0.7196	-0.3884	0.1609	0.0692	-0.0553	0.2883	0.0381	0.1932	-22.7181	16.8075	-10.1046
8	2.9018	0.1608	2.3055	0.5373	0.8063	6.653	-0.0597	0.0098	0.0088	0.0736	-0.0152	-0.0858	0.0383	-0.1656	0.0873	0.228	-0.0026	0.0038	0.1563	-0.0001	0.212	-49.7516	32.7083	28.1844
9	2.8802	0.247	-0.293	2.5818	0.7326	0.3829	0.1697	-0.6448	-0.4766	0.25	0.1049	-0.3047	0.5701	0.0222	-0.3049	0.3143	0.0599	0.0521	0.2842	0.1116	0.2862	-42.1839	23.3851	39.0218
10	2.3564	-0.9388	-0.6708	6.3696	1.407	2.5842	0.3536	0.3519	-0.3995	-0.0177	-0.4046	0.0586	0.9867	-0.2474	0.2195	0.4242	-0.0401	0.0048	0.2296	-0.0279	0.2926	-53.9915	20.0022	15.3273
11	2.3384	0.1226	2.5329	1.9049	0.9399	5.9615	0.0348	0.0451	-0.1876	0.0691	0.0291	0.0039	0.2903	0.1109	-0.0506	0.1947	0.0236	0.0361	0.1496	0.0264	0.1852	-42.4159	25.8267	27.3627
12	1.6718	0.2454	-0.2018	1.1085	-0.4022	5.3042	0.0425	-0.2813	-0.1187	0.0912	-0.0694	0.1133	0.4072	-0.4799	0.0041	0.1967	-0.0395	0.0302	0.2127	0.0345	0.254	-53.8988	26.7205	29.7004
13	1.2709	0.6288	0.9517	1.2312	0.1279	2.6361	-0.0406	0.1079	-0.17	-0.1941	-0.03	-0.098	-0.0715	0.0718	0.0689	0.195	0.0553	0.0456	0.2292	0.0126	0.2255	-33.1801	36.2793	1.7818
14	2.2662	3.6296	0.679	8.5682	-1.106	2.1058	0.1056	-0.2187	-0.6081	0.8118	-0.2073	-0.4721	-0.0303	0.8082	0.1174	0.3213	0.0762	-0.0416	0.4921	0.088	0.3811	-21.5454	36.4495	18.8881
15	2.5483	-0.2586	1.6241	1.362	0.0362	4.793	-0.0331	-0.0379	-0.0303	-0.0598	-0.1154	-0.1557	0.1235	0.0559	0.1371	0.1606	0.0585	0.0336	0.1808	0.0362	0.254	-33.2048	29.8288	5.399
16	0.2095	-0.0416	-0.6381	1.2409	0.0261	3.2951	-0.0274	0.0288	-0.0597	-0.1462	-0.0776	-0.1674	-0.0798	0.2823	0.0896	0.1292	0.016	0.0264	0.2259	0.0221	0.2102	-28.2169	39.9476	6.0582
17	1.9523	0.2578	-0.4712	1.7451	0.3994	2.145	-0.0974	-0.1757	0.0951	0.2868	-0.1276	0.0529	0.4385	0.1843	0.2404	0.2702	-0.0212	0.0222	0.2141	-0.0205	0.1847	6.731	13.5289	20.7378
18	3.9911	0.352	-2.8686	1.388	-1.5134	4.5833	0.064	-0.1483	0.0308	0.2757	0.0302	0.1877	0.0522	0.4942	-0.1093	0.2203	-0.066	0.0072	0.2093	-0.0189	0.1889	0.9327	15.6172	25.9582
19	1.9692	0.3371	-0.6779	1.2931	-1.439	2.0309	0.1946	-0.5928	0.4812	0.5202	0.0871	0.0494	-0.3907	0.0003	-0.2301	0.3903	-0.0608	0.0363	0.3598	-0.1349	0.2566	-1.0005	24.9158	32.9539
20	2.0915	0.7613	0.1637	6.1721	-0.7578	2.0635	0.0733	0.2566	0.2658	-0.6413	-0.3064	-0.2063	-0.448	0.5433	0.2484	0.3077	-0.0367	0.0402	0.2996	-0.021	0.2808	10.878	26.0058	9.4988
21	1.3431	0.7096	-1.3265	1.6212	-0.914	4.2216	0.031	-0.0878	0.1484	0.1457	0.0891	0.0794	-0.1561	-0.2047	-0.1288	0.2254	-0.0067	0.0405	0.2379	-0.0348	0.2451	-1.9109	22.9912	22.9132
22	1.5921	-0.1238	-0.2968	1.074	-0.5516	4.716	0.0793	-0.2211	0.0136	0.1187	-0.0859	-0.0688	0.0874	0.4139	0.006	0.1652	-0.0198	0.0027	0.2205	-0.0374	0.1875	8.5211	17.2602	19.8285
23	2.9302	0.8203	1.3755	3.586	-0.9044	3.8739	0.0995	-0.541	0.4006	0.2766	0.0427	0.091	-0.6961	0.1624	0.1921	0.4516	-0.258	0.0012	0.36	-0.303	0.2362	8.8919	27.2704	32.966

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1 THROUGH 17 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 18 THROUGH 33 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 34 THROUGH 50 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 51 THROUGH 61 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 62 THROUGH 102 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 103 THROUGH 133 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 134 THROUGH 144 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 1 THROUGH 26 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 27 THROUGH 42 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 43 THROUGH 50 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 51 THROUGH 102 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 103 THROUGH 144 )
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 1 THROUGH 42 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 43 THROUGH 50 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 51 THROUGH 95 )
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESID 96 THROUGH 144 )
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESID 1 THROUGH 17 )
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESID 18 THROUGH 26 )
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESID 27 THROUGH 42 )
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESID 43 THROUGH 50 )
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESID 51 THROUGH 95 )
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESID 96 THROUGH 133 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 134 THROUGH 144 )

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