PDB-6kge: Crystal structure of CaDoc0917(R16D)-CaCohA2 complex at pH 5.5

ID or keywords:

Entry

Database: PDB / ID: 6kge

Title

Crystal structure of CaDoc0917(R16D)-CaCohA2 complex at pH 5.5

Components

And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain
Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain

Keywords

HYDROLASE / cohesin / dockerin / cellulosome / calcium-binding

Function / homology

Function and homology information

cellulose binding / polysaccharide catabolic process / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function

Biological species

Clostridium acetobutylicum ATCC 824 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Feng, Y. / Yao, X.

Funding support

China, 2items

Citation

Journal: Sci Adv / Year: 2020
Title: Discovery and mechanism of a pH-dependent dual-binding-site switch in the interaction of a pair of protein modules.
Authors: Yao, X. / Chen, C. / Wang, Y. / Dong, S. / Liu, Y.J. / Li, Y. / Cui, Z. / Gong, W. / Perrett, S. / Yao, L. / Lamed, R. / Bayer, E.A. / Cui, Q. / Feng, Y.

History

Deposition	Jul 11, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 4, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6kge.cif.gz	236.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6kge.ent.gz	193.9 KB	Display	PDB format
PDBx/mmJSON format	6kge.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6kge_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	6kge_full_validation.pdf.gz	2.4 MB	Display
Data in XML	6kge_validation.xml.gz	18.6 KB	Display
Data in CIF	6kge_validation.cif.gz	27.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kg/6kge ftp://data.pdbj.org/pub/pdb/validation_reports/kg/6kge	HTTPS FTP

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Related structure data

Related structure data	6kg8C 6kg9C 6kgcC 6kgdC 6kgfC 1ohzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6kgd-d 1fap-d 3nts-2 5xgr-4 3a5p-2 6kgc-d 3ul4-d 6f0f-d 2d5v-1 1bxm-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) 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	#141 - Sep 2011 O-GlcNAc Transferase similarity (3) #74 - Feb 2006 alpha-Amylase similarity (2)

Deposited unit

C: Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain

D: And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain

A: Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain

B: And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain

hetero molecules

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

1

C: Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain

D: And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain

hetero molecules

defined by author&software
Evidence: gel filtration
22.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain

B: And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain

hetero molecules

defined by author&software
22.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	42.990, 76.030, 121.000
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Probably cellulosomal scaffolding protein, secreted cellulose-binding and cohesin domain Mass: 15624.421 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria) Strain: ATCC 824 / Gene: CA_C0910 / Plasmid: pET28a-SMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q977Y4
#2: Protein	And cellulose-binding endoglucanase family 9 CelL ortholog dockerin domain Mass: 6584.346 Da / Num. of mol.: 2 / Mutation: R16D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria) Strain: ATCC 824 / Gene: CA_C0917 / Plasmid: pET28a-SMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q97KK2
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.33 Å³/Da / Density % sol: 47.19 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.2 M MgCl2, 0.1 M sodium acetate, and 25% (w/v) PEG 3350 at pH 5.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.97915 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.97915 Å / Relative weight: 1

Reflection

Resolution: 2→35.751 Å / Num. obs: 51345 / % possible obs: 99.1 % / Redundancy: 3.725 % / B_iso Wilson estimate: 23 Å² / CC_1/2: 0.983 / R_merge(I) obs: 0.137 / R_rim(I) all: 0.16 / Χ²: 0.996 / Net I/σ(I): 6.47 / Num. measured all: 191254 / Scaling rejects: 6

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
2-2.05	3.743	0.407	3.38	14511	3881	3877	0.842	0.476	99.9
2.05-2.11	3.724	0.386	3.62	13804	3721	3707	0.854	0.452	99.6
2.11-2.17	3.75	0.331	4.15	13698	3657	3653	0.887	0.387	99.9
2.17-2.24	3.746	0.291	4.63	13176	3521	3517	0.898	0.34	99.9
2.24-2.31	3.712	0.27	4.93	12493	3382	3366	0.919	0.317	99.5
2.31-2.39	3.741	0.236	5.34	12438	3339	3325	0.942	0.276	99.6
2.39-2.48	3.734	0.235	5.39	11688	3144	3130	0.944	0.275	99.6
2.48-2.58	3.73	0.205	5.92	11425	3080	3063	0.948	0.24	99.4
2.58-2.7	3.731	0.194	6.2	10978	2964	2942	0.957	0.227	99.3
2.7-2.83	3.73	0.176	6.74	10380	2810	2783	0.953	0.206	99
2.83-2.98	3.702	0.15	7.44	9781	2672	2642	0.962	0.176	98.9
2.98-3.16	3.691	0.136	8.09	9191	2529	2490	0.97	0.159	98.5
3.16-3.38	3.672	0.13	8.94	8612	2381	2345	0.961	0.152	98.5
3.38-3.65	3.611	0.114	9.31	7835	2220	2170	0.972	0.135	97.7
3.65-4	3.621	0.107	9.76	7246	2028	2001	0.97	0.126	98.7
4-4.47	3.813	0.099	10.53	6879	1829	1804	0.98	0.115	98.6
4.47-5.16	3.811	0.101	10.66	6178	1637	1621	0.974	0.119	99
5.16-6.32	3.847	0.096	10.57	5228	1362	1359	0.981	0.112	99.8
6.32-8.94	3.808	0.087	10.75	4021	1063	1056	0.985	0.102	99.3
8.94-35.751	3.425	0.079	10.62	1692	578	494	0.98	0.093	85.5

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	(1.13_2998: ???)	refinement
Coot		model building
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1OHZ

1ohz

Resolution: 2→35.751 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.95
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection
R_free	0.2373	3742	7.29 %
R_work	0.1935	-	-
obs	0.1967	51340	99.13 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 150.99 Å² / B_iso mean: 34.2468 Å² / B_iso min: 11.21 Å²

Refinement step

Cycle: final / Resolution: 2→35.751 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2962	0	4	294	3260
B_iso mean	-	-	27.56	35.69	-
Num. residues	-	-	-	-	403

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2-2.0253	0.2868	140	0.2613	1805	100
2.0253-2.0519	0.317	142	0.258	1790	100
2.0519-2.08	0.2964	137	0.2597	1743	99
2.08-2.1097	0.2917	140	0.253	1794	100
2.1097-2.1412	0.2834	138	0.2445	1781	100
2.1412-2.1747	0.3621	138	0.252	1754	100
2.1747-2.2103	0.2808	143	0.2328	1772	100
2.2103-2.2484	0.2423	141	0.2312	1773	100
2.2484-2.2893	0.3056	139	0.2299	1797	99
2.2893-2.3333	0.2469	137	0.2159	1723	100
2.3333-2.381	0.231	142	0.2076	1805	100
2.381-2.4327	0.282	139	0.2116	1753	99
2.4327-2.4893	0.2928	143	0.2002	1770	100
2.4893-2.5515	0.2014	136	0.204	1767	99
2.5515-2.6205	0.3148	137	0.2138	1767	99
2.6205-2.6976	0.2484	139	0.2154	1768	99
2.6976-2.7846	0.2651	132	0.2122	1732	99
2.7846-2.8841	0.2816	143	0.2217	1776	99
2.8841-2.9995	0.2581	140	0.2068	1745	99
2.9995-3.136	0.266	140	0.2136	1758	99
3.136-3.3012	0.2586	142	0.1909	1773	99
3.3012-3.5078	0.1957	132	0.1911	1699	98
3.5078-3.7784	0.237	137	0.1612	1762	98
3.7784-4.1581	0.1947	144	0.1525	1767	99
4.1581-4.7586	0.1521	137	0.1373	1775	99
4.7586-5.9908	0.1654	137	0.142	1742	99
5.9908-35.751	0.2225	127	0.1786	1707	96

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	8.4298	6.6098	-1.3771	7.0938	-1.4877	3.2226	-0.0425	-0.425	0.2505	0.4681	0.0608	0.2422	-0.028	-0.1714	-0.1202	0.3023	0.027	0.0236	0.1602	-0.0181	0.1444	-11.4516	162.2783	54.87
2	8.0925	8.0668	-5.5209	8.6158	-5.7369	4.9214	0.3636	-0.3058	-0.1053	0.2265	-0.3124	-0.1125	-0.1191	0.2056	-0.0473	0.1418	0.027	-0.0135	0.1655	-0.0294	0.3013	-6.6499	168.4542	43.0314
3	7.0514	4.4329	-3.636	2.791	-2.294	1.8744	-0.1727	-0.0612	-0.925	-0.0714	-0.527	-1.7259	0.2921	0.6351	0.5782	0.1954	-0.0183	-0.0593	0.3007	0.007	0.423	2.1694	164.1689	46.4814
4	2.3346	1.6225	0.0584	3.3773	0.7664	1.676	0.1343	-0.3109	-0.3227	0.1936	-0.1648	-0.3309	0.3473	-0.0468	0.0454	0.2159	0.0329	-0.0469	0.1833	0.0168	0.3067	-7.3978	156.2359	48.4871
5	5.8027	3.7241	-0.4321	5.4314	-0.4095	1.763	-0.0811	-0.0387	0.164	0.0827	-0.0069	0.201	-0.0597	-0.037	0.1229	0.2178	0.0823	-0.0007	0.2455	-0.0421	0.2546	-11.0959	169.2089	47.3414
6	5.6323	4.2386	2.9892	7.4581	5.4688	7.591	0.2401	0.4574	-0.3538	0.0011	0.0289	-0.6115	0.3527	0.2867	-0.2959	0.218	0.0324	-0.0376	0.2087	-0.025	0.1999	-12.9834	147.037	29.4495
7	7.9144	-1.1571	-1.0532	5.6835	3.6229	5.1165	0.1329	0.0852	0.3463	-0.3813	-0.0703	-0.0765	-0.249	-0.0907	0.0383	0.204	0.0134	0.0122	0.1411	0.036	0.2364	-14.1647	155.1511	29.1962
8	5.9857	-1.5964	2.5546	4.9851	0.0081	6.4291	0.2662	-0.4985	-0.0667	0.4208	-0.5796	1.4449	0.2728	-0.786	-0.1878	0.2766	-0.0499	-0.007	0.3693	-0.041	0.2699	-19.5611	147.7754	38.5293
9	5.5895	3.5437	-4.8749	9.0275	-7.2302	6.6141	-0.0104	-0.0949	-0.423	0.0136	-0.1423	-0.4455	0.1852	-0.0208	0.1153	0.1922	-0.0584	-0.1106	0.1649	-0.0324	0.1867	15.899	147.0076	21.7595
10	3.8856	3.1959	-4.8509	7.6488	-7.9022	8.9731	-0.1678	-0.0014	-0.0273	-0.2807	-0.1891	-0.4255	0.4107	0.1537	0.3158	0.1405	-0.0297	-0.0576	0.1878	-0.0052	0.2127	18.6326	157.3592	17.3166
11	4.3461	4.9898	-3.1147	6.6174	-2.9547	3.077	0.0371	0.1008	-0.096	0.2405	0.0369	-0.1458	-0.0014	-0.0943	-0.1882	0.1581	0.0758	-0.0098	0.1408	0.0139	0.1782	6.7037	151.303	21.3305
12	7.0223	-6.7734	3.2079	7.8639	-2.4083	4.8039	-0.407	-0.4023	1.4704	0.9394	-0.093	-0.9919	-0.3584	0.0718	0.5675	0.3654	0.0101	-0.0948	0.205	-0.0023	0.4722	13.2602	168.4854	23.1113
13	2.3142	-0.9692	-0.2063	5.4598	-1.4256	2.837	-0.0187	-0.0743	0.1881	0.167	-0.0543	0.1999	-0.2448	0.1169	0.0278	0.2047	0.0129	-0.0395	0.1388	-0.0161	0.0909	9.634	163.4536	16.976
14	6.9982	6.7585	-6.589	7.1202	-6.4654	8.8973	0.2498	-0.1935	0.0446	0.2993	-0.0745	-0.0643	-0.2056	0.3571	-0.196	0.2414	0.0192	-0.0725	0.1198	0.0145	0.2348	12.5955	152.552	25.7025
15	2.0685	1.0346	-0.5362	8.6193	-4.7771	3.5464	0.1515	0.1082	-0.1296	-0.5597	-0.186	0.0893	0.3331	0.1412	0.008	0.2014	0.0197	-0.0097	0.1592	-0.0604	0.1837	11.7514	150.4283	14.1879
16	3.6399	-2.2114	0.9411	6.3367	-2.4935	8.2519	-0.0665	-0.132	0.3068	0.0317	0.2815	0.5247	-0.2468	-1.0418	-0.4049	0.1714	0.0096	0.0165	0.2704	0.0733	0.2998	-8.7265	176.7387	7.8861
17	4.2211	-2.1285	0.087	9.407	-4.7008	6.2411	0.1566	-0.6739	-0.0439	0.5509	0.1551	0.2953	-0.2832	0.1579	-0.1307	0.1521	0.0028	-0.0102	0.2471	0.0112	0.2027	-2.6936	169.8184	16.5124
18	5.1351	-4.2398	-3.3422	6.3428	0.135	4.6821	0.14	-0.3617	-0.4752	-0.228	0.4333	0.7304	0.3499	-0.7321	-0.2794	0.1925	-0.0308	0.0125	0.2882	0.0645	0.3947	-9.9294	166.8657	14.9657
19	4.5718	-2.7331	0.7177	3.3258	1.9059	6.0201	0.1732	0.2088	-0.0906	-0.5851	-0.3715	-0.4965	0.1002	0.3191	0.1225	0.1739	0.0168	-0.0341	0.2344	0.0165	0.1696	1.936	169.2204	6.3164
20	4.2808	4.6997	-3.1581	6.7975	-2.162	3.1826	0.2644	-0.4586	0.7586	0.3913	-0.1657	0.3053	-0.3883	0.3061	-0.1129	0.2988	0.016	-0.0726	0.1615	-0.0361	0.2606	-4.5393	171.2895	53.5653

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 35 )	A	20 - 35
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 47 )	A	36 - 47
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 55 )	A	48 - 55
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 56 through 105 )	A	56 - 105
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 145 )	A	106 - 145
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 26 )	B	1 - 26
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 27 through 47 )	B	27 - 47
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 48 through 60 )	B	48 - 60
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 5 through 19 )	C	5 - 19
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 20 through 35 )	C	20 - 35
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 36 through 55 )	C	36 - 55
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 56 through 67 )	C	56 - 67
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 68 through 95 )	C	68 - 95
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 96 through 105 )	C	96 - 105
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 106 through 145 )	C	106 - 145
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 0 through 14 )	D	0 - 14
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 15 through 26 )	D	15 - 26
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 27 through 37 )	D	27 - 37
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 38 through 60 )	D	38 - 60
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 5 through 19 )	A	5 - 19

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