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- PDB-6qj1: Crystal structure of the C. thermophilum condensin Smc2 ATPase he... -

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Basic information

Entry
Database: PDB / ID: 6qj1
TitleCrystal structure of the C. thermophilum condensin Smc2 ATPase head (crystal from I)
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: 2.56 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 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)49,0891
Polymers49,0891
Non-polymers00
Water73941
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 area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.320, 107.980, 174.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 49089.461 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.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.54 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% (w/v) PEG3350 0.2 M Succinate pH 7.0 2 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→45.893 Å / Num. obs: 31694 / % possible obs: 99.8 % / Redundancy: 16.095 % / Biso Wilson estimate: 72.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.084 / Χ2: 1.028 / Net I/σ(I): 20.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.5715.6421.8541.522400.5151.91697.6
2.57-2.6416.471.4112.1622530.7321.456100
2.64-2.7115.5361.1252.7321640.8071.163100
2.71-2.817.1470.8393.9121550.8930.864100
2.8-2.8917.2740.5895.7220410.9560.606100
2.89-2.9917.050.4357.5420200.9730.448100
2.99-3.116.8350.3259.9419250.9830.335100
3.1-3.2316.2260.22713.0318680.9910.235100
3.23-3.3715.5930.16616.518210.9950.172100
3.37-3.5417.3610.11324.1216850.9970.117100
3.54-3.7316.9230.09128.9516450.9980.094100
3.73-3.9616.7080.07433.8115790.9990.076100
3.96-4.2315.9720.06138.7814560.9990.063100
4.23-4.5715.420.05343.4813580.9990.054100
4.57-516.2830.05147.7612700.9990.052100
5-5.5915.3650.05446.2311580.9990.056100
5.59-6.4613.4180.05841.8710430.9990.06100
6.46-7.9113.8410.05247.118930.9990.054100
7.91-11.1913.3810.04451.97000.9990.046100
11.19-45.89311.2290.04248.744200.9990.04398.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
SHARPphasing
RefinementResolution: 2.56→45.893 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.94
RfactorNum. reflection% reflection
Rfree0.2621 1485 5 %
Rwork0.2326 --
obs0.2341 29681 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 251.99 Å2 / Biso mean: 88.7095 Å2 / Biso min: 46.72 Å2
Refinement stepCycle: final / Resolution: 2.56→45.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 0 41 3246
Biso mean---74.31 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033247
X-RAY DIFFRACTIONf_angle_d0.6294362
X-RAY DIFFRACTIONf_chiral_restr0.042506
X-RAY DIFFRACTIONf_plane_restr0.003555
X-RAY DIFFRACTIONf_dihedral_angle_d15.0862010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.56-2.64260.31341330.304225262659
2.6426-2.73710.33631330.308525112644
2.7371-2.84660.34041310.301525082639
2.8466-2.97620.31571340.288725362670
2.9762-3.1330.31961330.265425222655
3.133-3.32930.28651330.274925362669
3.3293-3.58630.27741340.259225512685
3.5863-3.9470.24221360.2425812717
3.947-4.51770.23751350.216425552690
4.5177-5.69010.24711370.205726162753
5.6901-45.90010.24861460.206127542900

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