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- PDB-6qj0: Crystal structure of the C. thermophilum condensin Smc2 ATPase he... -

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Basic information

Entry
Database: PDB / ID: 6qj0
TitleCrystal structure of the C. thermophilum condensin Smc2 ATPase head (crystal form II)
ComponentsStructural maintenance of chromosomes protein,Structural maintenance of chromosomes protein
KeywordsCELL CYCLE / condensin SMC complex ATPase chromosome condensation loop extrusion
Function / homology
Function and homology information


chromosome condensation / chromosome segregation / chromosome / cell division / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
Smc2, ATP-binding cassette domain / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHassler, M. / Haering, C.H.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilERC-2015-CoG 681365
CitationJournal: Mol.Cell / Year: 2019
Title: Structural Basis of an Asymmetric Condensin ATPase Cycle.
Authors: Hassler, M. / Shaltiel, I.A. / Kschonsak, M. / Simon, B. / Merkel, F. / Tharichen, L. / Bailey, H.J. / Macosek, J. / Bravo, S. / Metz, J. / Hennig, J. / Haering, C.H.
History
DepositionJan 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein


Theoretical massNumber of molelcules
Total (without water)46,3121
Polymers46,3121
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.745, 93.745, 117.971
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein


Mass: 46311.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0033000 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5H7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10-17 % (w/v) PEG 8,000, 0.1 M Na cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→81.186 Å / Num. all: 39710 / Num. obs: 39710 / % possible obs: 100 % / Redundancy: 10.3 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.103 / Rsym value: 0.098 / Net I/av σ(I): 3.8 / Net I/σ(I): 12.3 / Num. measured all: 409294
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2-2.1110.51.6490.557680.5331.7331.649100
2.11-2.2410.10.9080.854930.3010.9570.908100
2.24-2.3910.40.4931.651350.160.5190.493100
2.39-2.5810.50.3072.547600.0990.3220.307100
2.58-2.83100.1784.144290.0590.1880.178100
2.83-3.1610.60.114639860.0370.120.114100
3.16-3.65100.0797.535250.0260.0830.079100
3.65-4.4710.70.0688.129960.0220.0720.068100
4.47-6.3210.10.0648.323190.0210.0680.064100
6.32-81.18610.10.0646.812990.0210.0670.06499.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementResolution: 2→66.879 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.85
RfactorNum. reflection% reflection
Rfree0.2215 2000 5.04 %
Rwork0.1891 --
obs0.1907 39658 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.1 Å2 / Biso mean: 59.6872 Å2 / Biso min: 27.65 Å2
Refinement stepCycle: final / Resolution: 2→66.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 0 163 3333
Biso mean---55.71 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073219
X-RAY DIFFRACTIONf_angle_d0.8554328
X-RAY DIFFRACTIONf_chiral_restr0.051505
X-RAY DIFFRACTIONf_plane_restr0.004551
X-RAY DIFFRACTIONf_dihedral_angle_d17.9981998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.32571810.295226462827
2.05-2.10550.30131480.277326612809
2.1055-2.16740.31991410.267126862827
2.1674-2.23740.27241460.246627072853
2.2374-2.31740.27641180.232126532771
2.3174-2.41010.24331270.221727312858
2.4101-2.51980.27221340.221426802814
2.5198-2.65270.24141510.208426852836
2.6527-2.81890.24341430.20626792822
2.8189-3.03650.24651310.208827002831
3.0365-3.34210.24151350.206827142849
3.3421-3.82570.23011370.179426832820
3.8257-4.81980.18061530.146427072860
4.8198-66.91640.18811550.169327262881
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.12730.57940.18372.39490.31812.1954-0.06640.0062-0.24230.0567-0.0227-0.35170.03510.22940.07610.2408-0.01140.01620.35030.0590.3245-33.216848.612814.2987
25.7998-1.9528-3.2990.80021.07491.4325-0.6956-0.9133-0.73430.31260.28180.14870.28870.5150.4020.48590.05720.00320.78570.00890.5448-15.018119.672-21.6203
32.50910.25640.61782.77911.26363.5266-0.13690.0593-0.0057-0.5110.07480.1939-0.30140.05320.07260.305-0.0461-0.01750.2615-0.01290.3125-48.423249.33020.1694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 174 )A1 - 174
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 1050 )A175 - 1050
3X-RAY DIFFRACTION3chain 'A' and (resid 1051 through 1179 )A0

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