PDB-7v0i: Crystal structure of a CelR catalytic domain active site mutant w...

ID or keywords:

Entry

Database: PDB / ID: 7v0i

Title

Crystal structure of a CelR catalytic domain active site mutant with bound cellohexaose substrate

Components

Glucanase

Keywords

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

Function / homology

Function and homology information

Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose 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: 1.9 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	7v0i.cif.gz	794.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7v0i.ent.gz	672.6 KB	Display	PDB format
PDBx/mmJSON format	7v0i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7v0i_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	7v0i_full_validation.pdf.gz	2.4 MB	Display
Data in XML	7v0i_validation.xml.gz	52.7 KB	Display
Data in CIF	7v0i_validation.cif.gz	76 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/7v0i ftp://data.pdbj.org/pub/pdb/validation_reports/v0/7v0i	HTTPS FTP

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Related structure data

Related structure data	7unpSC 7v0jC 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

163 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
54.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glucanase

hetero molecules

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

3

C: Glucanase

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.302, 162.419, 210.522
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-642- HOH

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

Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 3 / Source method: obtained synthetically

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.49 Å³/Da / Density % sol: 50.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: JCSGD2B, 0.2M magnesium chloride, 0.1M HEPES buffer, pH 7.5, 30% PEG 400

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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: 1.9→39.87 Å / Num. obs: 125496 / % possible obs: 100 % / Redundancy: 7.471 % / B_iso Wilson estimate: 34.16 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.077 / R_rim(I) all: 0.082 / Χ²: 0.889 / Net I/σ(I): 16.86 / Num. measured all: 937581 / Scaling rejects: 40

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
1.9-1.95	7.507	1.348	1.4	69143	9216	9211	0.595	1.446	99.9
1.95-2	7.531	1.037	1.87	67384	8948	8947	0.724	1.113	100
2-2.06	7.545	0.776	2.57	65772	8718	8717	0.821	0.833	100
2.06-2.12	7.539	0.61	3.35	64096	8503	8502	0.876	0.654	100
2.12-2.19	7.563	0.48	4.35	62194	8223	8223	0.915	0.515	100
2.19-2.27	7.549	0.393	5.45	60187	7973	7973	0.94	0.421	100
2.27-2.36	7.531	0.312	6.89	57761	7670	7670	0.963	0.335	100
2.36-2.45	7.564	0.242	8.84	56243	7436	7436	0.975	0.26	100
2.45-2.56	7.529	0.193	11.25	53253	7073	7073	0.983	0.207	100
2.56-2.69	7.541	0.152	14.42	51465	6825	6825	0.989	0.163	100
2.69-2.83	7.514	0.124	17.5	48676	6479	6478	0.992	0.133	100
2.83-3	7.481	0.093	22.68	45981	6146	6146	0.995	0.1	100
3-3.21	7.437	0.072	28.2	43022	5785	5785	0.997	0.077	100
3.21-3.47	7.347	0.054	35.72	39658	5398	5398	0.998	0.058	100
3.47-3.8	7.33	0.042	43.18	36347	4960	4959	0.999	0.045	100
3.8-4.25	7.307	0.035	49.5	33152	4537	4537	0.999	0.037	100
4.25-4.91	7.313	0.03	52.44	29338	4012	4012	0.999	0.032	100
4.91-6.01	7.301	0.028	51.78	24822	3400	3400	0.999	0.03	100
6.01-8.5	7.188	0.023	53.91	19337	2691	2690	0.999	0.025	100
8.5-39.87	6.44	0.022	52.98	9750	1550	1514	0.999	0.024	97.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	1.9 Å	39.87 Å
Translation	1.9 Å	39.87 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: 1.9→39.87 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2324	3037	2.41 %
R_work	0.1854	122807	-
obs	0.1865	125496	99.8 %

Solvent computation

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

Displacement parameters

B_iso max: 206.4 Å² / B_iso mean: 49.4363 Å² / B_iso min: 21.02 Å²

Refinement step

Cycle: final / Resolution: 1.9→39.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10782	0	375	660	11817
B_iso mean	-	-	65.18	43.89	-
Num. residues	-	-	-	-	1353

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 (%)
1.9-1.93	0.3516	154	0.323	5359	5513	97
1.93-1.96	0.3051	153	0.3031	5517	5670	100
1.96-1.99	0.3316	153	0.2951	5557	5710	100
1.99-2.03	0.3332	150	0.2911	5535	5685	100
2.03-2.07	0.3116	82	0.2753	5561	5643	100
2.07-2.11	0.335	79	0.2654	5596	5675	100
2.11-2.16	0.3022	152	0.2542	5539	5691	100
2.16-2.21	0.3118	155	0.2464	5508	5663	100
2.21-2.26	0.3038	150	0.2391	5582	5732	100
2.26-2.32	0.2838	154	0.2259	5528	5682	100
2.32-2.39	0.2711	152	0.216	5562	5714	100
2.39-2.47	0.2742	150	0.22	5568	5718	100
2.47-2.56	0.2512	153	0.2117	5528	5681	100
2.56-2.66	0.2828	140	0.2002	5598	5738	100
2.66-2.78	0.3327	14	0.2019	5702	5716	100
2.78-2.92	0.2604	150	0.2018	5609	5759	100
2.93-3.11	0.2332	148	0.1978	5571	5719	100
3.11-3.35	0.2208	151	0.1869	5616	5767	100
3.35-3.68	0.2247	151	0.1633	5595	5746	100
3.68-4.22	0.1783	149	0.1415	5653	5802	100
4.22-5.31	0.1744	151	0.1274	5684	5835	100
5.31-39.87	0.1901	146	0.1518	5839	5985	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	0.4148	-0.1552	0.2712	0.3758	-0.3402	1.0879	-0.1921	-0.4139	-0.5991	0.1104	-0.2291	-0.5559	0.3166	0.2723	0.3204	0.4631	0.1157	0.1306	0.4386	0.2654	0.6523	10.791	-64.502	-20.287
2	2.3384	-0.7106	-0.1737	1.6113	-0.4481	2.3105	-0.1128	-0.6603	-0.3537	0.2657	-0.0799	-0.1193	0.2826	0.1164	0.1552	0.4867	0.0219	0.1252	0.4993	0.1399	0.3801	-5.745	-61.099	-9.703
3	2.0194	0.2067	0.4609	2.43	-0.8896	4.578	-0.2274	-0.2242	-0.1976	0.0657	0.1724	0.3288	0.5656	-0.998	-0.0299	0.2951	-0.0334	0.1305	0.3256	-0.0287	0.3347	-20.632	-56.569	-23.394
4	1.9757	1.2261	-0.9117	3.0044	-1.8248	2.4707	-0.1532	0.1053	-0.0986	-0.2872	0.0042	0.128	0.0707	-0.2425	0.162	0.3246	0.0212	0.0497	0.2902	-0.0277	0.235	-9.982	-49.182	-37.222
5	0.5065	0.0538	-0.0823	0.8986	-0.1023	1.1662	-0.1131	-0.0146	-0.2475	-0.0765	-0.0164	0.1336	0.2563	-0.2924	0.1088	0.3931	-0.0348	0.0989	0.3162	-0.0102	0.3768	-11.358	-61.79	-28.041
6	5.2001	4.0883	4.1615	5.5499	5.5837	5.6016	-0.4316	-0.5621	0.8571	0.6886	0.1354	-0.847	-0.2594	0.4079	0.3826	0.8638	0.087	-0.1767	0.3744	-0.0932	0.801	-5.829	-25.678	-25.264
7	5.3928	-0.9769	5.4508	9.3498	-0.0277	8.6399	-0.7672	-1.7198	0.2755	-0.1182	-0.2551	-0.4076	0.7463	-0.8522	0.9002	0.5976	0.186	0.1202	0.7231	0.0336	0.438	16.787	-32.308	-28.473
8	0.7091	1.4076	-2.0963	2.763	-4.1106	6.0974	-0.6495	-0.1683	0.0876	0.2182	-0.9181	-0.401	0.185	-0.016	1.414	0.4368	-0.0443	0.0553	0.6389	0.0256	0.5904	0.022	-48.334	-25.883
9	1.4784	-0.5892	-0.4181	2.7069	0.4502	1.2624	0.0837	0.0484	0.0871	-0.1324	-0.1946	0.2819	-0.1196	-0.2279	0.1028	0.2986	0.0815	-0.0525	0.3708	-0.1238	0.3206	-20.926	-19.771	-32.236
10	2.4559	-1.3428	0.5183	3.745	-1.1983	3.1148	-0.0265	-0.1515	-0.0826	0.4058	-0.1459	0.4151	0.0144	-0.3398	0.1619	0.3554	0.021	0.0585	0.4032	-0.1583	0.3343	-25.503	-22.084	-18.189
11	1.29	0.4926	-0.5149	2.0651	0.1854	1.7278	-0.0655	-0.6311	0.2683	0.4264	0.0175	0.0129	0.0892	0.1191	0.0117	0.4876	0.0906	-0.0312	0.5619	-0.2368	0.3934	-11.725	-11.258	-10.603
12	1.2952	-0.3841	-0.4485	3.1369	2.1264	3.207	0.0844	-0.0897	0.4313	-0.2575	0.1374	-0.2166	-0.3895	0.2457	-0.2232	0.3033	0.0144	0.0062	0.2261	-0.067	0.3224	-2.764	-11.401	-34.511
13	2.5315	-1.5193	-0.7373	5.6928	0.6374	1.5797	0.1932	-0.0718	0.5927	-0.3671	-0.0776	0.0927	-0.4089	-0.0981	-0.1188	0.4287	0.0484	-0.0136	0.2785	-0.1191	0.4087	-10.816	-6.535	-31.836
14	2.3155	0.137	-0.004	1.2815	0.1127	1.3229	-0.1458	0.1157	0.149	-0.172	0.0037	-0.1863	-0.2998	0.4315	0.141	0.3303	-0.0942	-0.0015	0.3909	0.0534	0.2441	28.832	-22.8	-38.04
15	4.7741	-0.5662	-0.2067	1.396	1.6512	2.9213	-0.1857	-0.439	0.7523	-0.0301	0.0666	0.0784	-0.3749	0.2291	0.1093	0.3457	-0.0841	-0.0614	0.363	-0.0125	0.2827	26.741	-15.228	-24.657
16	1.649	0.2448	0.2643	1.5743	0.5359	1.8209	-0.0569	-0.4222	-0.1464	0.2223	-0.0773	-0.29	-0.0223	0.4952	0.0984	0.2491	0.0185	-0.0215	0.568	0.126	0.3056	34.346	-35.036	-19.932
17	4.0142	-0.6958	1.3959	2.6598	-1.3647	1.5433	-0.1178	0.3158	-0.3556	-0.4448	0.0755	-0.1493	0.3425	0.1148	0.0653	0.2878	-0.0045	0.0723	0.254	-0.0385	0.2035	18.581	-40.84	-43.721
18	2.9688	-0.226	0.4412	1.9353	0.2252	0.9381	-0.0983	0.0907	-0.3358	-0.4567	-0.0377	-0.5138	0.0964	0.5553	0.0758	0.2749	0.0379	0.1014	0.4889	0.0778	0.367	34.655	-38.457	-37.123
19	1.5528	1.0881	-0.1292	1.7791	-0.428	1.0133	-0.3514	-0.0231	-0.5859	-0.3851	0.0352	-0.3531	0.5487	0.0165	0.2159	0.5068	0.06	0.2439	0.2288	0.0292	0.4583	0.751	-64.082	-33.556
20	7.6278	7.6534	3.0261	8.6019	4.528	4.4573	0.3362	0.0517	-0.8638	0.617	-0.324	-1.1398	0.8219	0.1247	-0.0151	0.5826	0.1783	0.2003	0.361	0.1883	0.6269	2.763	-73.638	-22.392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN C AND RESID 190:229 )	C	190 - 229
2	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 230:353 )	C	230 - 353
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 354:392 )	C	354 - 392
4	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 393:445 )	C	393 - 445
5	X-RAY DIFFRACTION	5	( CHAIN C AND RESID 446:469 )	C	446 - 469
6	X-RAY DIFFRACTION	6	( CHAIN D AND RESID 1:6 )	D	1 - 6
7	X-RAY DIFFRACTION	7	( CHAIN E AND RESID 1:6 )	E	1 - 6
8	X-RAY DIFFRACTION	8	( CHAIN F AND RESID 1:6 )	F	1 - 6
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 19:167 )	A	19 - 167
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 168:229 )	A	168 - 229
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 230:353 )	A	230 - 353
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 354:432 )	A	354 - 432
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 433:469 )	A	433 - 469
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 19:189 )	B	19 - 189
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 190:229 )	B	190 - 229
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 230:392 )	B	230 - 392
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 393:432 )	B	393 - 432
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 433:469 )	B	433 - 469
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 19:167 )	C	19 - 167
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 168:189 )	C	168 - 189

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Yorodumi