PDB-3l51: Crystal Structure of the Mouse Condensin Hinge Domain

ID or keywords:

Entry

Database: PDB / ID: 3l51

Title

Crystal Structure of the Mouse Condensin Hinge Domain

Components

Structural maintenance of chromosomes protein 2
Structural maintenance of chromosomes protein 4

Keywords

CELL CYCLE / Structural Maintenance of Chromosomes (SMC) / hinge domain / Cell division / Cytoplasm / DNA condensation / Mitosis / Nucleus

Function / homology

Function and homology information

Condensation of Prometaphase Chromosomes / positive regulation of chromosome condensation / positive regulation of chromosome separation / meiotic chromosome condensation / positive regulation of chromosome segregation / Condensation of Prophase Chromosomes / condensin complex / kinetochore organization / meiotic chromosome segregation / single strand break repair ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.506 Å

Authors

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

Citation

Journal: Nucleic Acids Res. / Year: 2010
Title: Structure and DNA binding activity of the mouse condensin hinge domain highlight common and diverse features of SMC proteins
Authors: Griese, J.J. / Witte, G. / Hopfner, K.-P.

History

Deposition	Dec 21, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 16, 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	3l51.cif.gz	160.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3l51.ent.gz	131.1 KB	Display	PDB format
PDBx/mmJSON format	3l51.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3l51_validation.pdf.gz	440.8 KB	Display	wwPDB validaton report
Full document	3l51_full_validation.pdf.gz	441.4 KB	Display
Data in XML	3l51_validation.xml.gz	18.1 KB	Display
Data in CIF	3l51_validation.cif.gz	27 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l5/3l51 ftp://data.pdbj.org/pub/pdb/validation_reports/l5/3l51	HTTPS FTP

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Related structure data

Similar structure data	3rb3-d 5j7k-2 4by5-1 4i2b-d 3gij-1 4f4w-1 3raq-2 4qze-d 4iqu-d 1s9f-3 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: Structural maintenance of chromosomes protein 2

B: Structural maintenance of chromosomes protein 4

hetero molecules

37.5 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)	33.455, 96.741, 54.537
Angle α, β, γ (deg.)	90.00, 92.84, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Structural maintenance of chromosomes protein 2 / SMC2 / Chromosome-associated protein E / XCAP-E homolog / FGF-inducible protein 16 Mass: 17946.188 Da / Num. of mol.: 1 / Fragment: hinge domain, residues 506-666 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: SMC2 (amino acids 506-666) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8CG48
#2: Protein	Structural maintenance of chromosomes protein 4 / SMC4 / Chromosome-associated polypeptide C / XCAP-C homolog Mass: 18985.287 Da / Num. of mol.: 1 / Fragment: hinge domain, residues 595-752 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: SMC4 (amino acids 595-752) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8CG47
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.39 Å³/Da / Density % sol: 48.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% PEG 4000, 5% isopropanol, 20% glycerol, 100mM Tris-HCl pH 8.5, 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: 0.9776 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9776 Å / Relative weight: 1
Reflection	Resolution: 1.506→29.133 Å / Num. all: 108029 / Num. obs: 53950 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / B_iso Wilson estimate: 13.46 Å² / R_sym value: 0.039 / Net I/σ(I): 21.43
Reflection shell	Resolution: 1.506→1.6 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 11.68 / Num. measured obs: 51194 / Num. unique all: 15878 / Num. unique obs: 16418 / R_sym value: 0.086 / % possible all: 90.6

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 1.51 Å / D res low: 27.89 Å / FOM acentric: 0.413 / FOM centric: 0.068 / Reflection acentric: 52585 / Reflection centric: 1236

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1.51	27.89	0	0	52585	1236
ANO_1	1.51	27.89	1.578	0	51285	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Reflection acentric	Reflection centric
ISO_1	6.57-27.89	0	605	61
ISO_1	4.71-6.57	0	1085	61
ISO_1	3.87-4.71	0	1390	62
ISO_1	3.36-3.87	0	1644	60
ISO_1	3.01-3.36	0	1876	60
ISO_1	2.75-3.01	0	2091	63
ISO_1	2.55-2.75	0	2245	63
ISO_1	2.38-2.55	0	2421	59
ISO_1	2.25-2.38	0	2559	61
ISO_1	2.13-2.25	0	2734	65
ISO_1	2.03-2.13	0	2807	61
ISO_1	1.95-2.03	0	2978	62
ISO_1	1.87-1.95	0	3012	55
ISO_1	1.8-1.87	0	3289	66
ISO_1	1.74-1.8	0	3361	63
ISO_1	1.69-1.74	0	3504	58
ISO_1	1.64-1.69	0	3625	67
ISO_1	1.59-1.64	0	3707	62
ISO_1	1.55-1.59	0	3838	65
ISO_1	1.51-1.55	0	3814	62
ANO_1	6.57-27.89	2.263	601	0
ANO_1	4.71-6.57	2.142	1076	0
ANO_1	3.87-4.71	1.732	1378	0
ANO_1	3.36-3.87	1.613	1620	0
ANO_1	3.01-3.36	1.842	1861	0
ANO_1	2.75-3.01	2.073	2071	0
ANO_1	2.55-2.75	2.008	2207	0
ANO_1	2.38-2.55	2	2384	0
ANO_1	2.25-2.38	1.389	2463	0
ANO_1	2.13-2.25	1.449	2653	0
ANO_1	2.03-2.13	1.196	2657	0
ANO_1	1.95-2.03	1.818	2927	0
ANO_1	1.87-1.95	1.017	2754	0
ANO_1	1.8-1.87	1.658	3248	0
ANO_1	1.74-1.8	1.684	3323	0
ANO_1	1.69-1.74	1.466	3451	0
ANO_1	1.64-1.69	1.401	3588	0
ANO_1	1.59-1.64	1.241	3667	0
ANO_1	1.55-1.59	1.06	3796	0
ANO_1	1.51-1.55	0.652	3560	0

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
6.57-27.89	0.511	0.088	605	61
4.71-6.57	0.485	0.067	1085	61
3.87-4.71	0.417	0.062	1390	62
3.36-3.87	0.398	0.061	1644	60
3.01-3.36	0.436	0.045	1876	60
2.75-3.01	0.464	0.059	2091	63
2.55-2.75	0.455	0.06	2245	63
2.38-2.55	0.455	0.071	2421	59
2.25-2.38	0.452	0.066	2559	61
2.13-2.25	0.45	0.057	2734	65
2.03-2.13	0.445	0.051	2807	61
1.95-2.03	0.442	0.069	2978	62
1.87-1.95	0.44	0.079	3012	55
1.8-1.87	0.435	0.074	3289	66
1.74-1.8	0.415	0.079	3361	63
1.69-1.74	0.407	0.067	3504	58
1.64-1.69	0.388	0.068	3625	67
1.59-1.64	0.355	0.071	3707	62
1.55-1.59	0.327	0.068	3838	65
1.51-1.55	0.324	0.095	3814	62

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 53820

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.2-100	66.3	0.776	512
5.4-7.2	56.7	0.908	688
4.51-5.4	57.7	0.925	871
3.95-4.51	59.5	0.931	1006
3.56-3.95	61.2	0.929	1125
3.26-3.56	59.9	0.924	1226
3.03-3.26	59.3	0.924	1316
2.84-3.03	59.2	0.92	1419
2.68-2.84	57.5	0.915	1544
2.55-2.68	57.3	0.922	1571
2.44-2.55	57.4	0.926	1690
2.33-2.44	55.9	0.927	1756
2.24-2.33	60.2	0.91	1783
2.16-2.24	59.2	0.912	1893
2.09-2.16	57.7	0.909	1918
2.03-2.09	62.9	0.905	1993
1.97-2.03	58.7	0.909	2066
1.91-1.97	62.5	0.894	2097
1.86-1.91	61.2	0.885	2139
1.82-1.86	59	0.886	2280
1.77-1.82	57.8	0.89	2315
1.73-1.77	57.2	0.881	2386
1.7-1.73	58.5	0.875	2435
1.66-1.7	57.7	0.868	2482
1.63-1.66	59.5	0.869	2568
1.6-1.63	61.9	0.855	2519
1.57-1.6	61.6	0.843	2673
1.54-1.57	65	0.797	2678
1.51-1.54	68.9	0.745	2871

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHARP		phasing
DM	6	phasing
PHENIX	1.5_2	refinement
PDB_EXTRACT	3.005	data extraction
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.506→29.133 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.17 / σ(F): 1.28 / Phase error: 14.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1729	5250	9.73 %	RANDOM
R_work	0.1429	-	-	-
obs	0.1459	53947	98.72 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.362 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso max: 50.56 Å² / B_iso mean: 17.204 Å² / B_iso min: 1.49 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.705 Å²	-0 Å²	-1.877 Å²
2-	-	0.712 Å²	0 Å²
3-	-	-	-0.007 Å²

Refinement step

Cycle: LAST / Resolution: 1.506→29.133 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2540	0	36	379	2955

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2740
X-RAY DIFFRACTION	f_angle_d	0.949	3721
X-RAY DIFFRACTION	f_chiral_restr	0.065	425
X-RAY DIFFRACTION	f_plane_restr	0.004	477
X-RAY DIFFRACTION	f_dihedral_angle_d	14.11	1050

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 (%)
1.5064-1.5235	0.2401	126	0.1817	1402	X-RAY DIFFRACTION	82
1.5235-1.5414	0.2209	146	0.1319	1548	X-RAY DIFFRACTION	97
1.5414-1.5602	0.1611	160	0.092	1697	X-RAY DIFFRACTION	100
1.5602-1.5799	0.145	174	0.0853	1643	X-RAY DIFFRACTION	100
1.5799-1.6007	0.1408	188	0.0795	1649	X-RAY DIFFRACTION	100
1.6007-1.6227	0.1491	170	0.0833	1623	X-RAY DIFFRACTION	100
1.6227-1.6458	0.1308	173	0.0863	1635	X-RAY DIFFRACTION	100
1.6458-1.6704	0.1597	177	0.094	1645	X-RAY DIFFRACTION	100
1.6704-1.6965	0.1662	167	0.0968	1643	X-RAY DIFFRACTION	100
1.6965-1.7243	0.1588	172	0.0992	1624	X-RAY DIFFRACTION	100
1.7243-1.754	0.1491	197	0.0955	1638	X-RAY DIFFRACTION	100
1.754-1.7859	0.1631	191	0.0998	1623	X-RAY DIFFRACTION	100
1.7859-1.8203	0.1648	182	0.0998	1632	X-RAY DIFFRACTION	100
1.8203-1.8574	0.1409	166	0.1036	1671	X-RAY DIFFRACTION	100
1.8574-1.8978	0.1656	170	0.1178	1618	X-RAY DIFFRACTION	99
1.8978-1.9419	0.1962	177	0.1523	1521	X-RAY DIFFRACTION	94
1.9419-1.9905	0.1731	176	0.1151	1637	X-RAY DIFFRACTION	99
1.9905-2.0443	0.1417	187	0.1103	1627	X-RAY DIFFRACTION	100
2.0443-2.1044	0.1711	169	0.1308	1596	X-RAY DIFFRACTION	96
2.1044-2.1723	0.1585	188	0.1187	1614	X-RAY DIFFRACTION	100
2.1723-2.25	0.1619	178	0.1335	1634	X-RAY DIFFRACTION	99
2.25-2.34	0.1957	184	0.1456	1590	X-RAY DIFFRACTION	98
2.34-2.4464	0.1755	177	0.1343	1640	X-RAY DIFFRACTION	100
2.4464-2.5754	0.1599	198	0.1416	1640	X-RAY DIFFRACTION	100
2.5754-2.7366	0.167	178	0.1424	1628	X-RAY DIFFRACTION	99
2.7366-2.9477	0.1607	179	0.1481	1633	X-RAY DIFFRACTION	100
2.9477-3.244	0.1902	168	0.1482	1666	X-RAY DIFFRACTION	100
3.244-3.7126	0.1462	186	0.1411	1647	X-RAY DIFFRACTION	100
3.7126-4.6744	0.1465	165	0.1403	1666	X-RAY DIFFRACTION	100
4.6744-29.138	0.1861	181	0.1784	1667	X-RAY DIFFRACTION	99

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