PDB-7v0j: Crystal structure of a CelR catalytic domain active site mutant w...

ID or keywords:

Entry

Database: PDB / ID: 7v0j

Title

Crystal structure of a CelR catalytic domain active site mutant with bound cellobiose product

Components

Glucanase

Keywords

HYDROLASE/PRODUCT / biomass deconstruction / glycoside hydrolase family 9 / GH9 / cellulose binding domain 3c / CBM3c / HYDROLASE / HYDROLASE-PRODUCT complex

Function / homology

Function and homology information

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

Biological species

Acetivibrio thermocellus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.4 Å

Authors

Bingman, C.A. / Kuch, N. / Kutsche, M.E. / Parker, A. / Smith, R.W. / Fox, B.G.

Funding support

United States, 2items

Organization	Grant number	Country
Department of Energy (DOE, United States)	DE-SC0018409	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32GM008349	United States

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Contribution of calcium ligands in substrate binding and product release in the Acetovibrio thermocellus glycoside hydrolase family 9 cellulase CelR.
Authors: Kuch, N.J. / Kutschke, M.E. / Parker, A. / Bingman, C.A. / Fox, B.G.

History

Deposition	May 10, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7v0j.cif.gz	772.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7v0j.ent.gz	656.2 KB	Display	PDB format
PDBx/mmJSON format	7v0j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7v0j_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	7v0j_full_validation.pdf.gz	1.3 MB	Display
Data in XML	7v0j_validation.xml.gz	46 KB	Display
Data in CIF	7v0j_validation.cif.gz	64 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/7v0j ftp://data.pdbj.org/pub/pdb/validation_reports/v0/7v0j	HTTPS FTP

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Related structure data

Related structure data	7unpSC 7v0iC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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
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: Glucanase

B: Glucanase

C: Glucanase

hetero molecules

161 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glucanase

hetero molecules

defined by author
Evidence: gel filtration
53.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glucanase

hetero molecules

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

3

C: Glucanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.585, 161.637, 210.439
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein

Glucanase

Mass: 53378.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acetivibrio thermocellus (bacteria) / Gene: Cthe_0578 / Production host:

Escherichia coli (E. coli)
References: UniProt: A3DCY5, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3 / Source method: obtained synthetically

#3: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

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: 2.46 Å³/Da / Density % sol: 49.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 19, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.4→40.17 Å / Num. obs: 118961 / % possible obs: 99.7 % / Redundancy: 3.858 % / B_iso Wilson estimate: 50.12 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.1 / R_rim(I) all: 0.117 / Χ²: 0.871 / Net I/σ(I): 9.8 / Num. measured all: 459004 / Scaling rejects: 93

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.4-2.46	3.888	1.347	1.02	34296	8835	8820	0.46	1.564	99.8
2.46-2.53	3.888	1.154	1.21	33476	8622	8611	0.552	1.339	99.9
2.53-2.6	3.896	0.878	1.56	32502	8354	8343	0.683	1.018	99.9
2.6-2.68	3.877	0.753	1.85	31306	8092	8075	0.723	0.873	99.8
2.68-2.77	3.897	0.666	2.16	30711	7889	7881	0.772	0.772	99.9
2.77-2.87	3.904	0.502	2.76	29827	7646	7640	0.861	0.581	99.9
2.87-2.98	3.902	0.393	3.56	28649	7353	7342	0.913	0.455	99.9
2.98-3.1	3.901	0.294	4.68	27511	7064	7052	0.954	0.341	99.8
3.1-3.24	3.907	0.223	6.05	26505	6800	6784	0.971	0.259	99.8
3.24-3.39	3.894	0.164	8.18	25045	6445	6431	0.982	0.19	99.8
3.39-3.58	3.844	0.118	11.22	23766	6217	6182	0.99	0.137	99.4
3.58-3.79	3.791	0.089	14.1	21629	5758	5706	0.994	0.104	99.1
3.79-4.06	3.782	0.064	18.56	20804	5534	5501	0.996	0.075	99.4
4.06-4.38	3.815	0.049	23.31	19324	5079	5065	0.997	0.057	99.7
4.38-4.8	3.799	0.045	25.17	17774	4694	4679	0.998	0.052	99.7
4.8-5.37	3.821	0.043	25.81	16216	4260	4244	0.998	0.05	99.6
5.37-6.2	3.791	0.042	26.36	14224	3759	3752	0.998	0.049	99.8
6.2-7.59	3.784	0.033	30.52	11849	3135	3131	0.998	0.039	99.9
7.59-10.73	3.762	0.022	36.54	9225	2456	2452	0.999	0.026	99.8
10.73-40.17	3.437	0.024	36.01	4365	1345	1270	0.999	0.028	94.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3.99 Å	40.17 Å
Translation	3.99 Å	40.17 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
XDS	Feb 5, 2021 BUILT=20210322	data reduction
XSCALE	Feb 5, 2021 BUILT=20210322	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7UNP

7unp

Resolution: 2.4→40.17 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2235	3061	4.94 %
R_work	0.1912	58897	-
obs	0.1928	61958	99.75 %

Solvent computation

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

Displacement parameters

B_iso max: 154.92 Å² / B_iso mean: 70.6041 Å² / B_iso min: 41.6 Å²

Refinement step

Cycle: final / Resolution: 2.4→40.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10818	0	138	170	11126
B_iso mean	-	-	94.54	56.02	-
Num. residues	-	-	-	-	1357

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4-2.44	0.3843	154	0.3543	2549	2703	96
2.44-2.48	0.3602	157	0.3375	2613	2770	100
2.48-2.52	0.3743	154	0.3122	2649	2803	100
2.52-2.56	0.3077	127	0.3056	2643	2770	100
2.56-2.61	0.3154	102	0.2749	2686	2788	100
2.61-2.67	0.3532	104	0.2734	2704	2808	100
2.67-2.72	0.33	133	0.275	2677	2810	100
2.72-2.79	0.2911	159	0.2572	2625	2784	100
2.79-2.86	0.3005	159	0.2491	2614	2773	100
2.86-2.93	0.2836	155	0.2502	2670	2825	100
2.93-3.02	0.2714	154	0.2402	2663	2817	100
3.02-3.12	0.2607	148	0.244	2659	2807	100
3.12-3.23	0.2942	149	0.242	2654	2803	100
3.23-3.36	0.2652	84	0.2211	2722	2806	100
3.36-3.51	0.2546	71	0.2104	2741	2812	100
3.51-3.7	0.2236	153	0.1936	2681	2834	100
3.7-3.93	0.2233	156	0.1793	2663	2819	100
3.93-4.23	0.2044	151	0.1415	2702	2853	100
4.23-4.66	0.1539	152	0.135	2695	2847	100
4.66-5.33	0.1794	151	0.1389	2692	2843	100
5.33-6.71	0.1763	148	0.1573	2761	2909	100
6.71-40.17	0.1535	140	0.1436	2834	2974	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	1.7198	-0.3703	-0.6087	3.5139	0.0574	1.5168	0.102	0.0758	0.1973	-0.25	-0.1403	0.2212	-0.3737	-0.2082	0.0458	0.6957	0.1069	-0.0589	0.4276	-0.0914	0.4269	-20.981	-18.095	-32.6391
2	3.532	-0.5848	0.3863	2.082	-0.3842	2.8777	-0.3118	-0.2326	-0.2322	0.2437	0.1338	0.2287	-0.0046	-0.2703	0.1863	0.6496	0.0566	0.0844	0.4321	-0.0814	0.459	-24.7672	-25.0738	-20.6308
3	2.4553	1.0621	-0.3424	1.6673	0.1094	0.7413	-0.0235	-0.5621	0.1989	0.2594	-0.0216	-0.0147	-0.0725	0.0742	0.0461	0.9798	0.0997	-0.0187	0.6629	-0.178	0.5187	-11.7904	-11.2661	-10.5616
4	1.2388	-0.1273	0.5116	2.555	1.3584	3.1298	-0.0239	-0.082	0.3844	-0.2896	0.0967	-0.2349	-0.6327	0.2406	-0.0552	0.801	-0.0104	0.0516	0.3771	-0.0529	0.451	-3.201	-12.5171	-34.0126
5	3.4601	-0.5654	0.022	2.7764	-3.1674	3.9075	0.0181	-0.1638	0.9989	0.1375	-0.2471	0.0781	-0.2181	-0.4629	0.1951	0.9818	0.0917	0.0043	0.335	-0.1044	0.8064	-14.0351	0.5302	-32.1877
6	9.0135	-7.3073	3.5754	7.954	-3.1869	3.8635	-0.3902	0.502	0.1466	0.2691	0.1942	-0.2848	-0.8315	0.4726	0.2091	0.8479	-0.18	0.1136	0.5871	-0.0745	0.4956	32.1634	-31.0885	-45.6658
7	2.8966	-0.0093	0.4391	1.3685	0.2596	1.581	-0.183	0.0141	0.3929	-0.0687	0.0591	-0.2011	-0.7035	0.3571	0.13	0.9282	-0.1908	0.0208	0.5413	0.0168	0.4627	27.6617	-20.3274	-35.666
8	6.4119	-0.9671	0.5131	3.2221	3.8688	5.3948	-0.1623	-0.37	0.7992	0.1689	0.1296	0.1322	-0.5955	0.2787	0.0461	0.8314	-0.0479	-0.0418	0.3896	0.0105	0.4306	26.5145	-15.2767	-24.5518
9	1.6218	-0.1924	-0.1091	3.3177	1.1766	1.6426	-0.057	-0.397	0.0937	0.3973	0.0845	-0.0513	-0.1383	0.3909	-0.0424	0.6868	-0.0622	-0.0514	0.7016	0.0549	0.4197	34.2622	-31.7522	-16.42
10	4.568	-1.3662	2.6014	0.861	-0.9966	3.0572	-0.1162	0.1117	-0.4056	-0.0917	0.1204	-0.0769	-0.0086	0.1449	-0.0324	0.5797	-0.0019	0.0606	0.3964	-0.0344	0.4877	25.7395	-43.3142	-38.0165
11	5.6514	-1.9216	0.3983	1.9491	-0.3356	3.4918	-0.1441	-0.0732	-0.1415	-0.0765	-0.1485	-0.435	0.0676	0.4368	0.3117	0.6199	-0.0642	0.1029	0.4644	0.0189	0.5773	34.2749	-38.3007	-38.2678
12	1.9158	0.6837	-0.1608	1.9677	0.0657	0.5627	-0.1852	0.0524	-0.4523	-0.0266	0.0447	-0.1884	0.2484	0.005	0.1358	0.7411	0.0342	0.093	0.3753	0.0016	0.5027	0.6131	-64.0349	-33.4475
13	4.0418	1.9986	1.042	1.7832	0.2526	2.4987	-0.0523	-0.2915	-0.6681	0.3153	0.0489	-0.6289	0.2372	0.0559	-0.008	0.7732	0.1284	0.0492	0.3809	0.0876	0.5962	8.0364	-67.2817	-20.8431
14	3.5476	-1.1621	0.2531	1.2226	-0.28	1.3425	-0.0748	-0.5794	-0.1873	0.357	0.016	-0.0956	0.2113	0.0158	0.0646	0.8999	0.0152	0.0904	0.5378	0.068	0.479	-5.9612	-60.8972	-9.5962
15	3.4346	-0.1417	0.5359	0.8026	1.1832	3.6082	-0.0686	-0.1907	-0.0607	0.2682	0.1474	0.5057	0.4059	-0.6422	-0.053	0.5964	0.0375	0.1512	0.4036	-0.0283	0.5202	-20.7633	-56.5449	-23.401
16	2.5966	0.8992	-1.0412	3.7922	-1.3751	4.395	-0.0191	0.076	-0.1444	-0.0344	0.0085	0.2918	-0.1468	-0.3852	0.0087	0.437	0.0335	0.0278	0.3335	-0.0349	0.3795	-13.0396	-55.1481	-35.3204
17	3.4192	-1.85	0.466	7.6888	-7.248	7.3826	-0.4915	-0.8767	1.6011	-0.9717	-1.8894	-0.2548	-0.3444	0.0053	1.9719	1.4734	-0.2628	-0.2633	0.769	-0.0228	0.9187	-5.2223	-29.2344	-32.6607
18	8.2778	2.7376	3.8127	5.278	5.2788	5.7053	-0.6072	-1.17	-0.483	1.4625	-0.1765	0.9998	0.5269	-0.879	0.7707	1.319	-0.1047	0.0003	0.7905	0.0496	0.8695	11.8961	-32.6921	-35.6111
19	9.8394	1.3719	4.7222	5.4204	-1.9279	6.0522	-1.1202	-0.4614	0.0234	-0.5461	-0.8372	1.1452	-0.1647	-0.488	1.8803	1.3356	0.2449	0.0652	1.1349	-0.3664	0.9737	0.7815	-45.6432	-33.4382

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 through 149 )	A	20 - 149
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 150 through 229 )	A	150 - 229
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 353 )	A	230 - 353
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 354 through 445 )	A	354 - 445
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 446 through 469 )	A	446 - 469
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 19 through 56 )	B	19 - 56
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 57 through 189 )	B	57 - 189
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 190 through 229 )	B	190 - 229
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 230 through 353 )	B	230 - 353
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 354 through 432 )	B	354 - 432
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 433 through 471 )	B	433 - 471
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 19 through 167 )	C	19 - 167
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 168 through 229 )	C	168 - 229
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 230 through 353 )	C	230 - 353
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 354 through 392 )	C	354 - 392
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 393 through 471 )	C	393 - 471
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 2)	D	1 - 2
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 1 through 2)	E	1 - 2
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 1 through 2)	F	1 - 2

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