PDB-3nwc: Crystal Structure of the Pyrococcus furiosus SMC Protein Hinge Domain

ID or keywords:

Entry

Database: PDB / ID: 3nwc

Title

Crystal Structure of the Pyrococcus furiosus SMC Protein Hinge Domain

Components

SMC protein

Keywords

CELL CYCLE / Structural Maintenance of Chromosomes (SMC) / SMC hinge domain / dimerization / DNA binding

Function / homology

Function and homology information

cohesin loader activity / sister chromatid cohesion / chromosome condensation / mitotic sister chromatid cohesion / chromosome segregation / chromosome / double-stranded DNA binding / DNA replication / ATP hydrolysis activity / DNA binding ...
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.6961 Å

Authors

Griese, J.J. / Hopfner, K.P.

Citation

Journal: Proteins / Year: 2011
Title: Structure and DNA-binding activity of the Pyrococcus furiosus SMC protein hinge domain
Authors: Griese, J.J. / Hopfner, K.P.

History

Deposition	Jul 9, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 20, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3nwc.cif.gz	87.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3nwc.ent.gz	68.9 KB	Display	PDB format
PDBx/mmJSON format	3nwc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3nwc_validation.pdf.gz	432.9 KB	Display	wwPDB validaton report
Full document	3nwc_full_validation.pdf.gz	436.8 KB	Display
Data in XML	3nwc_validation.xml.gz	17.7 KB	Display
Data in CIF	3nwc_validation.cif.gz	25.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nw/3nwc ftp://data.pdbj.org/pub/pdb/validation_reports/nw/3nwc	HTTPS FTP

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Related structure data

Similar structure data	5fcb-d 5fca-1 4mf6-1 4oz2-d 5fc1-d 5fc5-d 2h47-3 5fca-2 4oyo-d 4oym-d 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

Deposited unit

A: SMC protein

B: SMC protein

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

1

A: SMC protein

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

2

B: SMC protein

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

Unit cell

Length a, b, c (Å)	69.708, 118.653, 82.637
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-154- HOH

#1: Protein	SMC protein Mass: 21163.727 Da / Num. of mol.: 2 / Fragment: hinge domain, residues 488-667 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: SMC / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q877I1, UniProt: Q8TZY2*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

SMC protein

Mass: 21163.727 Da / Num. of mol.: 2 / Fragment: hinge domain, residues 488-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pyrococcus furiosus (archaea) / Gene: SMC / Plasmid: pET21 / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q877I1, UniProt: Q8TZY2*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.02 Å³/Da / Density % sol: 39.06 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.8M ammonium sulphate, 0.2M potassium-sodium tartrate, 0.1M trisodium citrate pH 6.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 0.9788, 0.9794, 0.9778

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2007

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9788	1
2	0.9794	1
3	0.9778	1

Reflection

Number: 418285 / R_merge(I) obs: 0.047 / D res high: 1.8 Å / Num. obs: 61802 / % possible obs: 99.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
5.33	35	2371	99.5	1	0.033
3.79	5.33	4243	100	1	0.031
3.1	3.79	5443	99.9	1	0.036
2.69	3.1	6454	100	1	0.045
2.41	2.69	7307	100	1	0.061
2.2	2.41	8086	100	1	0.085
2.04	2.2	8762	99.9	1	0.129
1.9	2.04	9481	99.9	1	0.217
1.8	1.9	9655	96.6	1	0.351

Reflection

Resolution: 1.6961→35 Å / Num. obs: 38299 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 22.98 Å² / R_merge(I) obs: 0.046 / Net I/σ(I): 24.02

Reflection shell

Resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.6961-1.8	0.227	0.336	4.7	75144	11853	11582	0.365	97.7
1.8-1.92	0.14	0.209	7.7	76469	11134	11132	0.226	100
1.92-2.08	0.081	0.121	13.3	71103	10391	10385	0.131	99.9
2.08-2.27	0.052	0.081	20.4	64195	9495	9491	0.087	100
2.27-2.54	0.033	0.056	29.6	60292	8647	8646	0.061	100
2.54-2.93	0.026	0.046	37.2	50699	7627	7626	0.05	100
2.93-3.58	0.019	0.037	48.5	43285	6450	6449	0.04	100
3.58-5.04	0.016	0.032	54.8	32184	4973	4973	0.034	100
5.04-35	0.015	0.033	57	18487	2808	2793	0.036	99.5

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.7 Å / D res low: 34.12 Å / FOM acentric: 0.419 / FOM centric: 0.166 / Reflection acentric: 34956 / Reflection centric: 3214

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1.7	34.12	0	0	29503	2867
ISO_2	1.7	34.12	0.449	0.331	29496	2866
ISO_3	1.7	34.12	0.132	0.102	29502	2866
ANO_1	1.7	34.12	2.161	0	29432	0
ANO_2	1.7	34.12	0.832	0	29504	0
ANO_3	1.7	34.12	1.776	0	34892	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	7.43-34.12	0	0	361	155
ISO_1	5.32-7.43	0	0	676	160
ISO_1	4.36-5.32	0	0	895	158
ISO_1	3.78-4.36	0	0	1079	162
ISO_1	3.39-3.78	0	0	1219	165
ISO_1	3.09-3.39	0	0	1361	156
ISO_1	2.87-3.09	0	0	1485	161
ISO_1	2.68-2.87	0	0	1595	155
ISO_1	2.53-2.68	0	0	1721	167
ISO_1	2.4-2.53	0	0	1798	166
ISO_1	2.29-2.4	0	0	1902	159
ISO_1	2.19-2.29	0	0	2009	155
ISO_1	2.11-2.19	0	0	2089	170
ISO_1	2.03-2.11	0	0	2163	159
ISO_1	1.96-2.03	0	0	2264	161
ISO_1	1.9-1.96	0	0	2336	164
ISO_1	1.84-1.9	0	0	2413	158
ISO_1	1.79-1.84	0	0	2137	136
ISO_1	1.74-1.79	0	0	0	0
ISO_1	1.7-1.74	0	0	0	0
ANO_1	7.43-34.12	4.251	0	361	0
ANO_1	5.32-7.43	7.269	0	674	0
ANO_1	4.36-5.32	5.128	0	895	0
ANO_1	3.78-4.36	3.649	0	1079	0
ANO_1	3.39-3.78	4.006	0	1218	0
ANO_1	3.09-3.39	3.921	0	1360	0
ANO_1	2.87-3.09	3.515	0	1485	0
ANO_1	2.68-2.87	3.487	0	1595	0
ANO_1	2.53-2.68	2.738	0	1720	0
ANO_1	2.4-2.53	2.332	0	1798	0
ANO_1	2.29-2.4	1.749	0	1901	0
ANO_1	2.19-2.29	1.388	0	2008	0
ANO_1	2.11-2.19	1.086	0	2088	0
ANO_1	2.03-2.11	0.826	0	2158	0
ANO_1	1.96-2.03	0.648	0	2264	0
ANO_1	1.9-1.96	0.526	0	2330	0
ANO_1	1.84-1.9	0.451	0	2412	0
ANO_1	1.79-1.84	0.355	0	2086	0
ANO_1	1.74-1.79	0	0	0	0
ANO_1	1.7-1.74	0	0	0	0
ISO_2	7.43-34.12	0.327	0.267	361	154
ISO_2	5.32-7.43	0.631	0.432	676	160
ISO_2	4.36-5.32	0.518	0.411	895	158
ISO_2	3.78-4.36	0.51	0.331	1079	162
ISO_2	3.39-3.78	0.506	0.345	1219	165
ISO_2	3.09-3.39	0.486	0.353	1361	156
ISO_2	2.87-3.09	0.514	0.385	1485	161
ISO_2	2.68-2.87	0.574	0.463	1595	155
ISO_2	2.53-2.68	0.556	0.401	1721	167
ISO_2	2.4-2.53	0.533	0.341	1798	166
ISO_2	2.29-2.4	0.494	0.363	1902	159
ISO_2	2.19-2.29	0.424	0.248	2009	155
ISO_2	2.11-2.19	0.352	0.245	2089	170
ISO_2	2.03-2.11	0.284	0.22	2163	159
ISO_2	1.96-2.03	0.233	0.167	2264	161
ISO_2	1.9-1.96	0.202	0.165	2336	164
ISO_2	1.84-1.9	0.182	0.143	2413	158
ISO_2	1.79-1.84	0.124	0.115	2130	136
ISO_2	1.74-1.79	0	0	0	0
ISO_2	1.7-1.74	0	0	0	0
ANO_2	7.43-34.12	2.318	0	361	0
ANO_2	5.32-7.43	2.712	0	676	0
ANO_2	4.36-5.32	1.814	0	895	0
ANO_2	3.78-4.36	1.571	0	1079	0
ANO_2	3.39-3.78	1.46	0	1218	0
ANO_2	3.09-3.39	1.644	0	1361	0
ANO_2	2.87-3.09	1.356	0	1483	0
ANO_2	2.68-2.87	1.323	0	1595	0
ANO_2	2.53-2.68	1.059	0	1721	0
ANO_2	2.4-2.53	0.874	0	1798	0
ANO_2	2.29-2.4	0.716	0	1902	0
ANO_2	2.19-2.29	0.506	0	2009	0
ANO_2	2.11-2.19	0.405	0	2088	0
ANO_2	2.03-2.11	0.316	0	2158	0
ANO_2	1.96-2.03	0.24	0	2264	0
ANO_2	1.9-1.96	0.195	0	2332	0
ANO_2	1.84-1.9	0.169	0	2412	0
ANO_2	1.79-1.84	0.11	0	2152	0
ANO_2	1.74-1.79	0	0	0	0
ANO_2	1.7-1.74	0	0	0	0
ISO_3	7.43-34.12	0.126	0.104	361	155
ISO_3	5.32-7.43	0.177	0.132	675	160
ISO_3	4.36-5.32	0.129	0.108	895	157
ISO_3	3.78-4.36	0.121	0.085	1079	162
ISO_3	3.39-3.78	0.116	0.075	1219	165
ISO_3	3.09-3.39	0.117	0.083	1361	156
ISO_3	2.87-3.09	0.119	0.093	1485	161
ISO_3	2.68-2.87	0.13	0.114	1595	155
ISO_3	2.53-2.68	0.126	0.102	1721	167
ISO_3	2.4-2.53	0.128	0.091	1798	166
ISO_3	2.29-2.4	0.122	0.095	1902	159
ISO_3	2.19-2.29	0.12	0.072	2009	155
ISO_3	2.11-2.19	0.113	0.083	2089	170
ISO_3	2.03-2.11	0.102	0.077	2163	159
ISO_3	1.96-2.03	0.093	0.062	2264	161
ISO_3	1.9-1.96	0.085	0.063	2336	164
ISO_3	1.84-1.9	0.079	0.055	2413	158
ISO_3	1.79-1.84	0.066	0.053	2137	136
ISO_3	1.74-1.79	0	0	0	0
ISO_3	1.7-1.74	0	0	0	0
ANO_3	7.43-34.12	4.003	0	360	0
ANO_3	5.32-7.43	4.899	0	673	0
ANO_3	4.36-5.32	3.734	0	895	0
ANO_3	3.78-4.36	3.039	0	1079	0
ANO_3	3.39-3.78	2.856	0	1219	0
ANO_3	3.09-3.39	3	0	1361	0
ANO_3	2.87-3.09	2.638	0	1484	0
ANO_3	2.68-2.87	2.683	0	1595	0
ANO_3	2.53-2.68	2.298	0	1721	0
ANO_3	2.4-2.53	2.117	0	1798	0
ANO_3	2.29-2.4	1.781	0	1901	0
ANO_3	2.19-2.29	1.414	0	2008	0
ANO_3	2.11-2.19	1.188	0	2088	0
ANO_3	2.03-2.11	0.931	0	2158	0
ANO_3	1.96-2.03	0.764	0	2264	0
ANO_3	1.9-1.96	0.616	0	2332	0
ANO_3	1.84-1.9	0.516	0	2412	0
ANO_3	1.79-1.84	0.42	0	2469	0
ANO_3	1.74-1.79	0.342	0	2541	0
ANO_3	1.7-1.74	0.28	0	2534	0

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
7.43-34.12	0.744	0.351	361	158
5.32-7.43	0.695	0.277	676	160
4.36-5.32	0.663	0.304	895	158
3.78-4.36	0.66	0.26	1079	162
3.39-3.78	0.678	0.255	1219	165
3.09-3.39	0.665	0.287	1361	157
2.87-3.09	0.654	0.214	1485	162
2.68-2.87	0.639	0.2	1595	155
2.53-2.68	0.593	0.172	1721	167
2.4-2.53	0.582	0.139	1798	166
2.29-2.4	0.544	0.13	1902	159
2.19-2.29	0.485	0.116	2009	155
2.11-2.19	0.44	0.111	2089	170
2.03-2.11	0.388	0.093	2163	159
1.96-2.03	0.331	0.066	2264	161
1.9-1.96	0.277	0.088	2336	164
1.84-1.9	0.237	0.074	2413	158
1.79-1.84	0.194	0.09	2470	162
1.74-1.79	0.129	0.061	2544	157
1.7-1.74	0.099	0.045	2576	159

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 38170

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.45-100	61.1	0.766	514
5.79-7.45	53.3	0.873	543
4.91-5.79	48	0.891	650
4.33-4.91	47.8	0.923	749
3.92-4.33	51.2	0.913	835
3.61-3.92	49.9	0.903	896
3.36-3.61	49.4	0.9	974
3.16-3.36	52.2	0.897	1029
2.99-3.16	54.1	0.897	1094
2.84-2.99	51.8	0.876	1140
2.71-2.84	52.1	0.889	1211
2.6-2.71	52.6	0.891	1259
2.51-2.6	57	0.889	1286
2.42-2.51	52.7	0.89	1371
2.34-2.42	58.6	0.893	1381
2.27-2.34	60	0.896	1428
2.2-2.27	61.7	0.889	1475
2.14-2.2	61.3	0.895	1526
2.09-2.14	65.1	0.891	1539
2.03-2.09	65.3	0.89	1605
1.99-2.03	67.2	0.884	1655
1.94-1.99	68.8	0.881	1679
1.9-1.94	72.6	0.876	1713
1.86-1.9	73.3	0.877	1729
1.82-1.86	73.8	0.86	1784
1.79-1.82	77.1	0.863	1811
1.76-1.79	80.2	0.831	1858
1.7-1.76	85.4	0.787	3436

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHARP		phasing
DM	6	phasing
PHENIX	1.6.1_357	refinement
PDB_EXTRACT	3.1	data extraction
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.6961→33.906 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.23 / σ(F): 2.07 / Phase error: 23.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2352	3818	10 %	random
R_work	0.194	34349	-	-
obs	0.1981	38167	99.67 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.609 Å² / k_sol: 0.343 e/Å³

Displacement parameters

B_iso max: 98.87 Å² / B_iso mean: 29.5331 Å² / B_iso min: 11.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.1478 Å²	-0 Å²	-0 Å²
2-	-	-7.3442 Å²	-0 Å²
3-	-	-	2.1964 Å²

Refinement step

Cycle: LAST / Resolution: 1.6961→33.906 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2758	0	0	251	3009

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2883
X-RAY DIFFRACTION	f_angle_d	0.991	3896
X-RAY DIFFRACTION	f_chiral_restr	0.066	451
X-RAY DIFFRACTION	f_plane_restr	0.004	509
X-RAY DIFFRACTION	f_dihedral_angle_d	13.51	1139

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6961-1.7176	0.2855	140	0.2449	1169	1309	92
1.7176-1.7402	0.3104	126	0.2509	1266	1392	100
1.7402-1.764	0.3266	134	0.2377	1277	1411	100
1.764-1.7892	0.2815	137	0.2359	1230	1367	100
1.7892-1.8159	0.2854	143	0.214	1256	1399	100
1.8159-1.8443	0.2958	149	0.2219	1261	1410	100
1.8443-1.8745	0.2917	152	0.2212	1244	1396	100
1.8745-1.9069	0.2659	138	0.2091	1269	1407	100
1.9069-1.9415	0.2556	144	0.2214	1250	1394	100
1.9415-1.9789	0.2785	141	0.2083	1272	1413	100
1.9789-2.0193	0.2704	140	0.2061	1261	1401	100
2.0193-2.0632	0.2632	143	0.2028	1264	1407	100
2.0632-2.1111	0.258	144	0.1983	1279	1423	100
2.1111-2.1639	0.2177	127	0.1883	1272	1399	100
2.1639-2.2224	0.2554	137	0.1988	1272	1409	100
2.2224-2.2878	0.2455	148	0.2035	1273	1421	100
2.2878-2.3616	0.2323	158	0.1919	1249	1407	100
2.3616-2.446	0.2648	135	0.209	1278	1413	100
2.446-2.5439	0.2591	146	0.199	1258	1404	100
2.5439-2.6597	0.2479	130	0.2037	1300	1430	100
2.6597-2.7998	0.2518	140	0.2022	1279	1419	100
2.7998-2.9751	0.2365	152	0.2023	1278	1430	100
2.9751-3.2047	0.2204	128	0.1919	1295	1423	100
3.2047-3.5269	0.2287	140	0.1785	1301	1441	100
3.5269-4.0365	0.1962	156	0.1615	1292	1448	100
4.0365-5.0829	0.1805	144	0.1534	1317	1461	100
5.0829-33.9125	0.2302	146	0.1991	1387	1533	100

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