PDB-4iu2: Cohesin-dockerin -X domain complex from Ruminococcus flavefacience

ID or keywords:

Entry

Database: PDB / ID: 4iu2

Title

Cohesin-dockerin -X domain complex from Ruminococcus flavefacience

Components

Cell-wall anchoring protein
Cellulose-binding protein

Keywords

STRUCTURAL PROTEIN / Beta sandwich / cellulose degradation

Function / homology

Function and homology information

polysaccharide catabolic process / carbohydrate binding / membrane / metal ion binding
Similarity search - Function

Biological species

Ruminococcus flavefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.001 Å

Authors

Salama-Alber, O. / Bayer, E. / Frolow, F.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Atypical Cohesin-Dockerin Complex Responsible for Cell Surface Attachment of Cellulosomal Components: BINDING FIDELITY, PROMISCUITY, AND STRUCTURAL BUTTRESSES.
Authors: Salama-Alber, O. / Jobby, M.K. / Chitayat, S. / Smith, S.P. / White, B.A. / Shimon, L.J. / Lamed, R. / Frolow, F. / Bayer, E.A.

History

Deposition	Jan 19, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4iu2.cif.gz	198.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4iu2.ent.gz	167.7 KB	Display	PDB format
PDBx/mmJSON format	4iu2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4iu2_validation.pdf.gz	445.4 KB	Display	wwPDB validaton report
Full document	4iu2_full_validation.pdf.gz	447.4 KB	Display
Data in XML	4iu2_validation.xml.gz	24.6 KB	Display
Data in CIF	4iu2_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iu/4iu2 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iu2	HTTPS FTP

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Related structure data

Related structure data	4iu3C C: citing same article (ref.)
Similar structure data	2itd-d 2hjf-d 2dwd-d 6w0j-d 3whi-3 6w0f-d 2itc-d 3iga-d 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 (1)

Deposited unit

A: Cell-wall anchoring protein

B: Cellulose-binding protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.714, 78.714, 203.238
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

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Protein , 2 types, 2 molecules AB

#1: Protein	Cell-wall anchoring protein Mass: 22946.514 Da / Num. of mol.: 1 / Fragment: UNP residues 29-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Gene: scaE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0AEF6
#2: Protein	Cellulose-binding protein Mass: 26599.607 Da / Num. of mol.: 1 / Fragment: UNP residues 565-803 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Gene: cttA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0AEF5

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Non-polymers , 4 types, 629 molecules

#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 618 / 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: 3.18 Å³/Da / Density % sol: 61.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, ammonium sulfate 1.8 M, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97841 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97841 Å / Relative weight: 1
Reflection	Resolution: 2→20.03 Å / Num. obs: 44177 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / R_merge(I) obs: 0.137 / R_sym value: 0.137 / Net I/σ(I): 17.1

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHELXS		phasing
PHENIX	(phenix.refine: dev_1269)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.001→20.03 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 18.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1956	2085	5.04 %	RANDOM
R_work	0.153	-	-	-
all	0.1552	76982	-	-
obs	0.1552	44058	93.56 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.001→20.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3409	0	31	618	4058

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3595
X-RAY DIFFRACTION	f_angle_d	0.945	4938
X-RAY DIFFRACTION	f_dihedral_angle_d	11.896	1259
X-RAY DIFFRACTION	f_chiral_restr	0.065	542
X-RAY DIFFRACTION	f_plane_restr	0.004	643

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 (%)
2.0014-2.0258	0.2615	126	0.2305	2434	X-RAY DIFFRACTION	85
2.0258-2.0515	0.2805	158	0.2239	2292	X-RAY DIFFRACTION	85
2.0515-2.0785	0.232	143	0.2121	2431	X-RAY DIFFRACTION	87
2.0785-2.1069	0.2464	140	0.2041	2414	X-RAY DIFFRACTION	88
2.1069-2.137	0.2217	108	0.2005	2552	X-RAY DIFFRACTION	89
2.137-2.1689	0.2438	143	0.1905	2395	X-RAY DIFFRACTION	87
2.1689-2.2028	0.2554	118	0.1801	2513	X-RAY DIFFRACTION	89
2.2028-2.2389	0.2446	135	0.1771	2521	X-RAY DIFFRACTION	91
2.2389-2.2775	0.1857	153	0.1722	2567	X-RAY DIFFRACTION	94
2.2775-2.3189	0.1983	154	0.1675	2571	X-RAY DIFFRACTION	89
2.3189-2.3635	0.2186	123	0.1676	2501	X-RAY DIFFRACTION	91
2.3635-2.4117	0.2401	100	0.173	2598	X-RAY DIFFRACTION	92
2.4117-2.4641	0.2092	141	0.1634	2553	X-RAY DIFFRACTION	92
2.4641-2.5214	0.1897	133	0.1603	2580	X-RAY DIFFRACTION	93
2.5214-2.5844	0.2132	162	0.1656	2588	X-RAY DIFFRACTION	93
2.5844-2.6542	0.2436	114	0.1633	2674	X-RAY DIFFRACTION	95
2.6542-2.7323	0.21	144	0.1617	2687	X-RAY DIFFRACTION	96
2.7323-2.8204	0.2151	155	0.1649	2638	X-RAY DIFFRACTION	96
2.8204-2.9211	0.2159	146	0.1578	2766	X-RAY DIFFRACTION	97
2.9211-3.0379	0.2153	154	0.1628	2693	X-RAY DIFFRACTION	97
3.0379-3.176	0.1791	148	0.1489	2728	X-RAY DIFFRACTION	98
3.176-3.3432	0.1857	150	0.1488	2727	X-RAY DIFFRACTION	99
3.3432-3.5524	0.181	152	0.1391	2743	X-RAY DIFFRACTION	99
3.5524-3.8261	0.1595	143	0.12	2802	X-RAY DIFFRACTION	99
3.8261-4.2101	0.16	146	0.1144	2749	X-RAY DIFFRACTION	99
4.2101-4.8168	0.1292	130	0.1095	2770	X-RAY DIFFRACTION	99
4.8168-6.0595	0.1747	131	0.1275	2821	X-RAY DIFFRACTION	100
6.0595-28.9388	0.1829	131	0.155	2793	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	4.1534	-1.7021	2.2135	1.975	-0.7293	1.9117	-0.0421	0.02	0.2355	0.0395	-0.011	-0.0305	-0.444	-0.0544	0.1134	0.2567	0.0006	0.0352	0.168	-0.0217	0.1876	74.1345	68.9045	52.7631
2	3.5798	0.2839	2.75	1.5194	-1.0017	8.8134	-0.1135	0.636	-0.0581	-0.6641	0.1166	-0.1108	-0.3506	0.1847	0.0337	0.3891	0.0357	0.0196	0.2171	-0.0262	0.1622	74.7709	60.0165	30.4019
3	2.7653	-0.7028	1.3514	1.557	-0.4813	3.5072	-0.0034	0.0059	-0.102	-0.0546	-0.0184	0.039	0.032	-0.0159	0.0131	0.1102	0.0086	0.0251	0.1027	0.0018	0.1239	76.6031	50.5359	46.7686
4	1.3356	-0.148	0.1683	1.5445	0.1402	2.3909	0.0354	0.0109	0.0557	-0.0851	-0.0474	0.0307	-0.235	-0.0628	0.0181	0.11	-0.0071	0.0209	0.107	0.0049	0.1219	76.4224	60.4088	48.8172
5	2.6796	-1.2535	1.1062	3.2871	-2.129	6.3913	0.1249	0.2185	0.2939	-0.5023	-0.1293	-0.0063	-0.6453	-0.1393	0.0651	0.3238	0.0628	-0.0044	0.1462	0.0349	0.2191	72.2261	70.4741	38.6872
6	4.1022	0.4975	1.0533	3.4512	-0.3192	3.6593	0.0614	0.9462	0.7901	-0.8734	0.124	0.1707	-0.595	-0.0865	0.0592	0.5281	0.0703	-0.0105	0.3298	0.1437	0.2419	71.5324	67.6507	26.6727
7	4.1228	-1.4414	-3.6134	1.8767	1.0287	3.3888	0.0323	-0.4009	-0.0568	0.3658	-0.1292	0.3284	0.1626	-0.1656	0.1699	0.2465	-0.0652	0.0651	0.3642	-0.0275	0.2542	62.1861	41.8319	114.0259
8	0.6744	-0.0602	-0.757	0.9202	-0.2937	4.9754	-0.0357	-0.0508	0.1814	0.0364	0.0114	0.1259	0.1423	-0.2726	0.0497	0.1122	-0.0182	0.0075	0.24	-0.0061	0.2172	62.9803	40.8288	101.9517
9	2.9924	1.0064	-2.4535	2.9947	-1.3125	6.0716	0.2382	-0.1355	0.1705	0.231	-0.0071	0.1313	-0.528	-0.0031	-0.2198	0.1758	0.0059	0.0097	0.1963	0.0035	0.1839	66.969	47.7358	90.9494
10	1.3783	-0.2094	-0.5184	1.6619	-0.3314	2.8026	-0.1289	-0.2103	-0.2158	0.1993	0.0255	-0.0201	0.3335	0.2137	0.0486	0.2007	0.0249	0.0334	0.19	0.0426	0.1529	77.9835	40.6783	69.7198
11	4.096	-2.3689	-0.8057	4.1323	-2.8037	5.2171	-0.0459	-0.3535	-0.3927	0.3761	0.36	1.1208	0.2394	-0.6256	-0.1432	0.1964	-0.0361	0.06	0.2947	0.0545	0.3498	61.1249	44.9459	61.0794

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 33 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 51 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 52 through 124 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 190 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 191 through 202 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 203 through 212 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 5 through 19 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 20 through 84 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 85 through 120 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 121 through 217 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 218 through 242 )

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