PDB-8x39: Crystal structure of cellulosomal double-dockerin module of Clo13...

ID or keywords:

Entry

Database: PDB / ID: 8x39

Title

Crystal structure of cellulosomal double-dockerin module of Clo1313_0689 from Clostridium thermocellum

Components

Serine protease

Keywords

PROTEIN BINDING / CALCIUM-BINDING PROTEIN

Function / homology

Function and homology information

polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function

Biological species

Acetivibrio thermocellus DSM 1313 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Chen, C. / Dong, S. / Feng, Y.

Funding support

China, 1items

Citation

Journal: Protein Sci. / Year: 2024
Title: A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features.
Authors: Chen, C. / Yang, H. / Dong, S. / You, C. / Morais, S. / Bayer, E.A. / Liu, Y.J. / Xuan, J. / Cui, Q. / Mizrahi, I. / Feng, Y.

History

Deposition	Nov 12, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8x39.cif.gz	207.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8x39.ent.gz	139 KB	Display	PDB format
PDBx/mmJSON format	8x39.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8x39_validation.pdf.gz	4 MB	Display	wwPDB validaton report
Full document	8x39_full_validation.pdf.gz	4 MB	Display
Data in XML	8x39_validation.xml.gz	15.5 KB	Display
Data in CIF	8x39_validation.cif.gz	23.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x3/8x39 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/8x39	HTTPS FTP

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Related structure data

Related structure data	8x3aC 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	#184 - Apr 2015 Glucagon similarity (11) #142 - Oct 2011 PDB Pioneers similarity (11)

Deposited unit

A: Serine protease

B: Serine protease

hetero molecules

33.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	58.160, 68.950, 74.000
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Serine protease Mass: 16489.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The taxonomy was provided by the authors. Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria) Gene: cprA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2HPT9
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.25 Å³/Da / Density % sol: 45.32 %
Crystal grow	Temperature: 316 K / Method: vapor diffusion, sitting drop Details: 0.1 M bis-Tris, 25% (w/v) polyethylene glycol 3,350, 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: BL19U1 / Wavelength: 0.97849 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97849 Å / Relative weight: 1
Reflection	Resolution: 1.7→45.73 Å / Num. obs: 63223 / % possible obs: 99.93 % / Redundancy: 6.68 % / B_iso Wilson estimate: 21.34 Å² / CC_1/2: 0.998 / Net I/σ(I): 13.23
Reflection shell	Resolution: 1.7→1.74 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4690 / CC_1/2: 0.846

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHASER		phasing
PHENIX		model building
PHENIX	1.20.1_4487	refinement
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→45.73 Å / SU ML: 0.1783 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7345
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2033	3744	5.92 %
R_work	0.1658	59465	-
obs	0.168	63209	99.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→45.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2099	0	8	337	2444

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0103	2123
X-RAY DIFFRACTION	f_angle_d	1.0125	2878
X-RAY DIFFRACTION	f_chiral_restr	0.062	338
X-RAY DIFFRACTION	f_plane_restr	0.0077	379
X-RAY DIFFRACTION	f_dihedral_angle_d	5.1621	295

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 (%)
1.7-1.72	0.2874	144	0.2432	2211	X-RAY DIFFRACTION	99.54
1.72-1.74	0.2892	150	0.2517	2189	X-RAY DIFFRACTION	99.96
1.74-1.77	0.2933	122	0.2183	2254	X-RAY DIFFRACTION	100
1.77-1.79	0.2573	138	0.2167	2145	X-RAY DIFFRACTION	99.96
1.79-1.82	0.2241	135	0.2116	2232	X-RAY DIFFRACTION	99.96
1.82-1.85	0.2316	145	0.2004	2195	X-RAY DIFFRACTION	100
1.85-1.88	0.198	134	0.2068	2236	X-RAY DIFFRACTION	99.96
1.88-1.91	0.2341	138	0.1987	2190	X-RAY DIFFRACTION	99.83
1.91-1.95	0.2674	134	0.1975	2209	X-RAY DIFFRACTION	100
1.95-1.98	0.2027	138	0.1865	2162	X-RAY DIFFRACTION	99.96
1.98-2.02	0.2323	158	0.1808	2204	X-RAY DIFFRACTION	100
2.02-2.07	0.2146	120	0.1674	2209	X-RAY DIFFRACTION	99.96
2.07-2.12	0.2191	149	0.1722	2196	X-RAY DIFFRACTION	99.96
2.12-2.17	0.2073	140	0.1632	2225	X-RAY DIFFRACTION	99.87
2.17-2.23	0.2084	132	0.1554	2191	X-RAY DIFFRACTION	99.87
2.23-2.29	0.1567	126	0.1577	2233	X-RAY DIFFRACTION	100
2.29-2.37	0.2053	122	0.1621	2215	X-RAY DIFFRACTION	99.96
2.37-2.45	0.1563	163	0.1564	2165	X-RAY DIFFRACTION	99.96
2.45-2.55	0.2218	133	0.156	2235	X-RAY DIFFRACTION	100
2.55-2.67	0.1781	144	0.1491	2182	X-RAY DIFFRACTION	100
2.67-2.81	0.2178	122	0.1699	2202	X-RAY DIFFRACTION	99.91
2.81-2.98	0.2129	156	0.1777	2198	X-RAY DIFFRACTION	100
2.98-3.21	0.2459	144	0.1626	2209	X-RAY DIFFRACTION	99.92
3.21-3.54	0.2022	141	0.1553	2187	X-RAY DIFFRACTION	99.91
3.54-4.05	0.1599	147	0.1396	2197	X-RAY DIFFRACTION	99.87
4.05-5.1	0.1759	126	0.1379	2200	X-RAY DIFFRACTION	99.79
5.1-45.73	0.2027	143	0.1789	2194	X-RAY DIFFRACTION	99.36

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	4.40077716726	1.76973893968	-3.26054011606	3.99161392981	-4.85797432894	6.45212177344	-0.0732395613858	-0.0671408857495	-0.107947556497	-0.213549221304	-0.028979003142	-0.211970411291	0.284275397925	0.3517102684	0.0801296744217	0.159441773349	0.0394205455979	0.0161205784655	0.157475541284	-0.00334150034546	0.141467314506	22.0344248328	33.8504209382	58.693904967
2	8.1796280094	-6.74664781377	-5.49755441851	9.54655915348	5.75050876703	4.21720073528	-0.245332485345	-0.700734870877	-0.388588938328	0.469228421348	0.00496341994321	0.206339431511	0.0712946207755	0.829724444595	0.213354253066	0.198657425764	0.0129510159828	-0.0281924623739	0.285188144013	0.0300812337132	0.190131828146	19.8414991177	36.2571874266	71.1336895683
3	9.00041284655	-6.34759245311	1.98016871568	9.88008736052	2.77924060609	8.41255435963	-0.72278335167	-0.301626069005	1.11807728277	1.03220159343	-0.0113846972781	-0.667319197159	-1.22747659359	0.436635397454	0.65654769943	0.603797925967	-0.0399229066446	-0.0548375881633	0.538686445118	-0.155476404176	0.757200847055	22.0287315679	44.315939417	72.7453560067
4	6.69087291637	-0.530453935189	0.401731787439	7.40568029934	-1.85533531594	3.69740778926	-0.157538277383	0.00597446015421	-0.016077956265	-0.270409795925	0.0153375591328	-0.193333598612	-0.0544436789667	-0.0407577995682	0.132267916494	0.120660587594	-0.0141197472382	0.000286061985916	0.125573159902	0.0198457594176	0.112123507879	28.4315238166	61.7703615565	33.5190580313
5	1.78972866976	-0.000427534599846	-0.89088821848	3.2016608154	-1.79766995989	6.7377139902	-0.0817685650575	-0.0561912802012	0.0908753023695	-0.0309056284295	-0.00409091729593	0.0473340362065	-0.251874981905	-0.00564976801846	0.0746771545125	0.0894855201566	0.00291857566578	-0.0227471614755	0.119296647237	-0.0179211401435	0.151502798909	21.0781401714	63.8046940623	33.8191516811
6	1.69869653352	-1.84016234021	2.83695619092	3.73088392015	-2.48128118998	4.83726775751	0.0808483302173	-0.0795278309666	0.0565699654392	-0.480344269334	0.233983922991	0.171765578453	0.577213352048	-0.236428955189	-0.357631481744	0.3104109995	-0.0130082387047	-0.0167204455187	0.25941895349	0.0398949221182	0.276072808831	18.7562026008	57.6206908749	19.5912951101
7	5.02282629947	-1.50442055715	1.57447364011	4.4978829477	-1.00534087209	5.96186145832	-0.0726317046133	-0.0178396982291	-0.0286511108088	0.219379740554	0.073180037449	-0.0186962733374	0.034864212454	-0.123238658519	0.0193911770779	0.12676134889	-0.00432071236035	0.0189773944126	0.134733980268	0.0187730860812	0.117557213412	18.72159623	68.8146417595	13.4688648558
8	3.25119600476	4.93468533515	3.4840586511	7.53676032289	5.19015125888	5.94278802024	-0.231133460004	0.220385883168	-0.212089833925	-0.0434640031381	0.237786565156	-0.0827200280127	0.406120584307	0.28962149835	0.012880522369	0.222136430684	0.0120834373704	0.0551125135114	0.26759969087	0.0515841970917	0.249673144371	22.1685638562	63.2409517695	3.57387385542
9	7.85818817987	2.16160812213	-3.56400502739	8.14290486708	-2.02994095636	4.45682862114	0.129856123914	-0.394818234515	0.183536091671	0.480118431648	0.0246766956269	-0.238211806328	-0.295249121889	0.495407799951	-0.155029427492	0.192544191346	0.00774725033475	-0.0279870662694	0.162103783604	-0.00260979771656	0.166566333155	27.4597555436	48.0884102558	45.0838429019
10	3.05846351864	-1.99813751442	-0.943301230827	9.83856245949	-0.813524096087	7.97456179279	-0.111084782723	-0.0238106899261	-0.345660729369	-0.0989515114307	0.0166716527286	-0.194831296795	0.355348554119	0.226373002886	0.084726035652	0.108163014368	0.0198301850723	0.0251960641643	0.124152489304	0.0154354049857	0.164609011853	29.7920145399	37.0787005708	39.6150750788
11	3.15775679678	0.104152611133	0.205494863785	3.44349682501	1.09941377132	6.59314484421	-0.0915694594364	-0.196942175767	-0.180347336435	0.0650507344225	0.0164796138838	-0.0531801134456	0.15371508067	0.14487188402	0.0660600559558	0.108514981412	0.0126584655551	0.0223791723594	0.121393294996	0.0458247975791	0.128785461777	22.7589083699	36.6848989809	47.2600567872
12	2.60097411322	2.60476831013	-1.2726449092	7.50182515854	-2.89326989199	5.86752484318	-0.142960440437	0.0505610257417	-0.00637772455815	-0.360782076251	0.0295433627469	0.00230481713101	0.0925317885513	-0.307352396281	0.133445439934	0.105699558113	0.00451704624964	-0.0229190712881	0.150545037166	-0.00540042441012	0.133643538936	20.0424304157	43.6104523888	35.0091637506
13	3.95294406679	2.9551859064	-3.91701505761	3.0673082657	-1.49205300155	6.25243364332	0.0859999718255	-0.0623415400253	-0.0185759951048	0.134200010443	0.0758025212732	0.0522983242275	-0.00165549575624	-0.0582425234806	-0.148126455164	0.297884285718	0.0017866047942	0.0384027203435	0.200930949931	0.0187386737314	0.265152411898	17.5321069358	45.7528688963	55.422399789
14	7.36667264232	-3.61892703886	5.92778768003	2.04515011528	-2.46342165431	8.59924455722	-0.300010511692	0.379482550394	0.566128452049	-0.304300670406	-0.111872598712	0.437048184843	-0.502149119525	-0.318645563864	0.432440981597	0.32764439908	0.00834085053011	-0.00628036370975	0.252539984156	0.0291803568652	0.276787438588	10.0629188641	42.5552159759	62.3733560307
15	3.62431511008	-4.83465928251	0.625027088629	7.77482435342	1.52838599018	4.64572708308	-0.087223079783	-0.389873820641	-0.0450240721829	0.178126615815	0.262944473619	0.270992957005	0.0163439928178	-0.211591095156	-0.155482575432	0.217929841944	-0.0483947741137	0.0511846584118	0.215887076318	0.0215162859601	0.230664888829	13.8929321463	31.2679310715	64.7034144064

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 99 through 120 )	B	G	99 - 120	98 - 119
2	2	chain 'B' and (resid 121 through 132 )	B	G	121 - 132	120 - 131
3	3	chain 'B' and (resid 133 through 139 )	B	G	133 - 139	132 - 138
4	4	chain 'A' and (resid 2 through 27 )	A	A	2 - 27	1 - 26
5	5	chain 'A' and (resid 28 through 69 )	A	A	28 - 69	27 - 68
6	6	chain 'A' and (resid 70 through 79 )	A	A	70 - 79	69 - 78
7	7	chain 'A' and (resid 80 through 120 )	A	A	80 - 120	79 - 119
8	8	chain 'A' and (resid 121 through 140 )	A	A	121 - 140	120 - 139
9	9	chain 'B' and (resid 2 through 15 )	B	G	2 - 15	1 - 14
10	10	chain 'B' and (resid 16 through 27 )	B	G	16 - 27	15 - 26
11	11	chain 'B' and (resid 28 through 48 )	B	G	28 - 48	27 - 47
12	12	chain 'B' and (resid 49 through 69 )	B	G	49 - 69	48 - 68
13	13	chain 'B' and (resid 70 through 79 )	B	G	70 - 79	69 - 78
14	14	chain 'B' and (resid 80 through 86 )	B	G	80 - 86	79 - 85
15	15	chain 'B' and (resid 87 through 98 )	B	G	87 - 98	86 - 97

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