PDB-4n2o: Structure of a novel autonomous cohesin protein from Ruminococcus...

ID or keywords:

Entry

Database: PDB / ID: 4n2o

Title

Structure of a novel autonomous cohesin protein from Ruminococcus flavefaciens

Components

Autonomous cohesin

Keywords

STRUCTURAL PROTEIN / Nine-stranded beta sandwich /

cohesin /

Dockerin

Function / homology

Immunoglobulin-like - #680 /

Immunoglobulin-like /

Sandwich / Mainly Beta / Autonomous cohesin

Function and homology information

Biological species

Ruminococcus flavefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.442 Å

Authors

Frolow, F. / Voronov-Goldman, M. / Levy-Assaraf, M. / Lamed, R. / Bayer, E. / Shimon, L.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structural characterization of a novel autonomous cohesin from Ruminococcus flavefaciens.
Authors: Voronov-Goldman, M. / Levy-Assaraf, M. / Yaniv, O. / Wisserman, G. / Jindou, S. / Borovok, I. / Bayer, E.A. / Lamed, R. / Shimon, L.J. / Frolow, F.

History

Deposition	Oct 5, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 9, 2014	Group: Database references
Revision 1.2	May 14, 2014	Group: Database references
Revision 1.3	Jul 17, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4n2o.cif.gz	610 KB	Display	PDBx/mmCIF format
PDB format	pdb4n2o.ent.gz	530.2 KB	Display	PDB format
PDBx/mmJSON format	4n2o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n2/4n2o ftp://data.pdbj.org/pub/pdb/validation_reports/n2/4n2o	HTTPS FTP

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Related structure data

Similar structure data	4zz6-d 6th0-1 5zyh-d 7d2o-d 3v70-1 5x07-4 5mr7-1 1mzw-d 6yts-d 5ur3-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Autonomous cohesin

B: Autonomous cohesin

C: Autonomous cohesin

D: Autonomous cohesin

E: Autonomous cohesin

F: Autonomous cohesin

G: Autonomous cohesin

H: Autonomous cohesin

hetero molecules

183 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Autonomous cohesin

hetero molecules

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

2

B: Autonomous cohesin

hetero molecules

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

3

C: Autonomous cohesin

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

4

D: Autonomous cohesin

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

5

E: Autonomous cohesin

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

6

F: Autonomous cohesin

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

7

G: Autonomous cohesin

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

8

H: Autonomous cohesin

hetero molecules

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

9

A: Autonomous cohesin

B: Autonomous cohesin

hetero molecules

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

10

C: Autonomous cohesin

D: Autonomous cohesin

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

11

E: Autonomous cohesin

F: Autonomous cohesin

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

12

G: Autonomous cohesin

H: Autonomous cohesin

hetero molecules

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

Unit cell

Length a, b, c (Å)	116.240, 67.726, 258.907
Angle α, β, γ (deg.)	90.00, 93.08, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-440- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	4 - 195
2	1	B	4 - 195
1	2	A	8 - 195
2	2	C	8 - 195
1	3	A	4 - 193
2	3	D	4 - 193
1	4	A	6 - 194
2	4	E	6 - 194
1	5	A	7 - 195
2	5	F	7 - 195
1	6	A	5 - 195
2	6	G	5 - 195
1	7	A	6 - 195
2	7	H	6 - 195
1	8	B	8 - 195
2	8	C	8 - 195
1	9	B	4 - 193
2	9	D	4 - 193
1	10	B	6 - 194
2	10	E	6 - 194
1	11	B	7 - 195
2	11	F	7 - 195
1	12	B	5 - 195
2	12	G	5 - 195
1	13	B	6 - 195
2	13	H	6 - 195
1	14	C	8 - 193
2	14	D	8 - 193
1	15	C	8 - 194
2	15	E	8 - 194
1	16	C	8 - 196
2	16	F	8 - 196
1	17	C	8 - 195
2	17	G	8 - 195
1	18	C	8 - 195
2	18	H	8 - 195
1	19	D	6 - 193
2	19	E	6 - 193
1	20	D	7 - 193
2	20	F	7 - 193
1	21	D	5 - 193
2	21	G	5 - 193
1	22	D	6 - 193
2	22	H	6 - 193
1	23	E	7 - 194
2	23	F	7 - 194
1	24	E	6 - 194
2	24	G	6 - 194
1	25	E	6 - 194
2	25	H	6 - 194
1	26	F	7 - 195
2	26	G	7 - 195
1	27	F	7 - 195
2	27	H	7 - 195
1	28	G	6 - 195
2	28	H	6 - 195

NCS ensembles :

#1: Protein	Autonomous cohesin Mass: 22845.656 Da / Num. of mol.: 8 / Fragment: RfCohG module residue numbers 26-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Plasmid: pET28(+) / Production host: Escherichia coli (E. coli) / References: UniProt: W5IDC3*PLUS
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.78 Å³/Da / Density % sol: 55.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 9 ul drop containing 2 ul of SeMet-RfCohG-CH solution (13mg/ml) and 7 ul reservoir solution (0.1 M Sodium Acetate pH 5 and 6% w/v Polyethylene glycol 4000), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2009 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.44→22.77 Å / Num. all: 72856 / Num. obs: 72856 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / R_merge(I) obs: 0.14 / R_sym value: 0.13 / Net I/σ(I): 24

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
SHELXS		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
DENZO		data reduction
SCALEPACK		data scaling
X-QUBE		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2.442→22.77 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.926 / SU B: 18.104 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22889	3678	5.1 %	RANDOM
R_work	0.20537	-	-	-
obs	0.2066	69119	96.81 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 46.744 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.92 Å²	0 Å²	0.21 Å²
2-	-	-1.32 Å²	0 Å²
3-	-	-	3.2 Å²

Refinement step

Cycle: LAST / Resolution: 2.442→22.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11858	0	4	383	12245

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	12143
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	11088
X-RAY DIFFRACTION	r_angle_refined_deg	1.529	1.976	16488
X-RAY DIFFRACTION	r_angle_other_deg	2.166	3	25680
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.291	5	1703
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.031	26.547	585
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.351	15	1733
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.68	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1798
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	15257
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	2783
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.809	1.984	6147
X-RAY DIFFRACTION	r_mcbond_other	2.799	1.984	6146
X-RAY DIFFRACTION	r_mcangle_it	4.21	2.961	7675
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.532	2.356	5996
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	10908	0.07
1	2	B	10908	0.07
2	1	A	10486	0.09
2	2	C	10486	0.09
3	1	A	10442	0.09
3	2	D	10442	0.09
4	1	A	10476	0.1
4	2	E	10476	0.1
5	1	A	10482	0.1
5	2	F	10482	0.1
6	1	A	10819	0.07
6	2	G	10819	0.07
7	1	A	10714	0.07
7	2	H	10714	0.07
8	1	B	10356	0.1
8	2	C	10356	0.1
9	1	B	10676	0.09
9	2	D	10676	0.09
10	1	B	10698	0.09
10	2	E	10698	0.09
11	1	B	10479	0.1
11	2	F	10479	0.1
12	1	B	10821	0.08
12	2	G	10821	0.08
13	1	B	10984	0.07
13	2	H	10984	0.07
14	1	C	10242	0.1
14	2	D	10242	0.1
15	1	C	10334	0.11
15	2	E	10334	0.11
16	1	C	10363	0.11
16	2	F	10363	0.11
17	1	C	10390	0.1
17	2	G	10390	0.1
18	1	C	10267	0.1
18	2	H	10267	0.1
19	1	D	10664	0.09
19	2	E	10664	0.09
20	1	D	10093	0.11
20	2	F	10093	0.11
21	1	D	10345	0.1
21	2	G	10345	0.1
22	1	D	10402	0.09
22	2	H	10402	0.09
23	1	E	10167	0.11
23	2	F	10167	0.11
24	1	E	10298	0.11
24	2	G	10298	0.11
25	1	E	10462	0.1
25	2	H	10462	0.1
26	1	F	10520	0.09
26	2	G	10520	0.09
27	1	F	10505	0.1
27	2	H	10505	0.1
28	1	G	10795	0.08
28	2	H	10795	0.08

LS refinement shell

Resolution: 2.442→2.505 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.301	183	-
R_work	0.301	3499	-
obs	-	-	65.99 %

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	1.0257	0.2735	-0.6188	1.5275	-0.731	1.8283	-0.0718	0.0043	-0.0672	0.0114	-0.0131	-0.0816	-0.0397	0.1003	0.0849	0.1876	0.0096	-0.0189	0.1886	-0.0096	0.0105	11.645	-0.413	127.256
2	2.4384	0.0564	-0.991	1.473	0.2033	1.681	-0.1511	0.1058	-0.2021	-0.075	0.0344	-0.0455	0.1294	-0.0588	0.1167	0.2798	-0.0482	0.0125	0.2109	-0.0415	0.0244	10.67	-9.631	102.531
3	1.7047	0.2143	-0.6504	1.8237	0.589	2.5163	-0.073	0.3444	0.0592	-0.4672	-0.0061	-0.0456	-0.4068	-0.0722	0.079	0.3964	-0.0608	-0.031	0.3169	0.0177	0.0139	29.608	18.531	89.614
4	2.4591	0.9405	-0.7235	2.3815	-0.6414	3.1817	-0.1837	0.1612	-0.2358	-0.4475	-0.0921	-0.3725	-0.1062	0.1985	0.2758	0.4481	0.0052	0.1506	0.4235	-0.0426	0.105	43.592	3.719	72.729
5	2.2866	-0.3652	1.2803	1.7228	-0.7867	3.4431	0.1074	-0.444	0.1507	0.2119	-0.1117	-0.0682	0.3595	-0.1033	0.0043	0.4084	-0.0031	-0.0888	0.5442	-0.1426	0.0596	50.071	45.815	57.342
6	2.6973	-0.1168	0.5514	2.0262	0.3519	2.7643	-0.0133	-0.4743	-0.0723	0.443	-0.0217	0.0198	0.2984	-0.1288	0.0351	0.3003	0.0236	0.0126	0.2753	0.0009	0.0038	36.421	30.954	39.123
7	1.0539	-0.2839	0.6521	1.439	-0.7319	1.7537	-0.069	0.0232	0.0538	0.0031	0.0196	-0.0625	0.0284	0.1207	0.0493	0.1646	-0.0021	-0.0068	0.1506	-0.0082	0.005	18.437	50.532	2.071
8	2.0566	-0.205	0.6807	1.144	0.189	1.2254	-0.1328	-0.1345	0.2046	0.0529	0.0893	-0.0951	-0.119	-0.0274	0.0435	0.2608	0.0417	-0.0259	0.1958	-0.0637	0.0367	17.429	59.365	26.954

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 196
2	X-RAY DIFFRACTION	1	A	301
3	X-RAY DIFFRACTION	1	A	401 - 474
4	X-RAY DIFFRACTION	2	B	4 - 196
5	X-RAY DIFFRACTION	2	B	301
6	X-RAY DIFFRACTION	2	B	401 - 458
7	X-RAY DIFFRACTION	3	C	8 - 197
8	X-RAY DIFFRACTION	3	C	301 - 351
9	X-RAY DIFFRACTION	4	D	4 - 194
10	X-RAY DIFFRACTION	4	D	301 - 306
11	X-RAY DIFFRACTION	5	E	6 - 195
12	X-RAY DIFFRACTION	5	E	301 - 308
13	X-RAY DIFFRACTION	6	F	7 - 199
14	X-RAY DIFFRACTION	6	F	301 - 353
15	X-RAY DIFFRACTION	7	G	5 - 196
16	X-RAY DIFFRACTION	7	G	301 - 369
17	X-RAY DIFFRACTION	8	H	6 - 196
18	X-RAY DIFFRACTION	8	H	301
19	X-RAY DIFFRACTION	8	H	401 - 464

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