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- PDB-6qj3: Crystal structure of the C. thermophilum condensin Ycs4-Brn1 subc... -

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Basic information

Entry
Database: PDB / ID: 6qj3
TitleCrystal structure of the C. thermophilum condensin Ycs4-Brn1 subcomplex
Components
  • Brn1
  • Condensin complex subunit 1,Condensin complex subunit 1,Ycs4
  • Condensin complex subunit 2
KeywordsCELL CYCLE / condensin SMC complex ATPase chromosome condensation loop extrusion
Function / homology
Function and homology information


condensin complex / mitotic chromosome condensation / chromosome / cell division / nucleus / cytoplasm
Similarity search - Function
Condensin subunit 1 / Condensin complex subunit 1, N-terminal / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / non-SMC mitotic condensation complex subunit 1 / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Condensin complex subunit 1 / Condensin complex subunit 2
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.3 Å
AuthorsHassler, M. / Haering, C.H. / Kschonsak, M.
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 16, 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: Condensin complex subunit 1,Condensin complex subunit 1,Ycs4
B: Condensin complex subunit 2
C: Brn1


Theoretical massNumber of molelcules
Total (without water)153,9533
Polymers153,9533
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-50 kcal/mol
Surface area51230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.615, 81.760, 132.878
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Condensin complex subunit 1,Condensin complex subunit 1,Ycs4


Mass: 130546.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Chaetomium thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0049230 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SB82
#2: Protein Condensin complex subunit 2


Mass: 21686.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053810 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SBJ6
#3: Protein/peptide Brn1


Mass: 1720.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli)
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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: 13% (w/v) PEG 8,000, 0.1 M ADA pH 7.1, 0.13 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.3→45.11 Å / Num. obs: 27912 / % possible obs: 99.3 % / Redundancy: 12.6 % / Rmerge F obs: 0.175 / Rpim(I) all: 0.073 / Rrim(I) all: 0.19 / Net I/σ(I): 11.5
Reflection shellResolution: 3.3→3.5 Å / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4321 / Rpim(I) all: 0.645 / Rrim(I) all: 1.1287

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.3→45.11 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.01
RfactorNum. reflection% reflection
Rfree0.2841 1984 7.11 %
Rwork0.2305 --
obs0.2343 27912 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7700 0 0 0 7700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047809
X-RAY DIFFRACTIONf_angle_d0.85410591
X-RAY DIFFRACTIONf_dihedral_angle_d5.384756
X-RAY DIFFRACTIONf_chiral_restr0.0421283
X-RAY DIFFRACTIONf_plane_restr0.0051355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3039-3.38650.36351250.3281689X-RAY DIFFRACTION92
3.3865-3.4780.37631380.29891846X-RAY DIFFRACTION100
3.478-3.58030.34651480.2861833X-RAY DIFFRACTION100
3.5803-3.69580.31011370.26481863X-RAY DIFFRACTION100
3.6958-3.82780.34351460.24331831X-RAY DIFFRACTION100
3.8278-3.9810.25881460.22141859X-RAY DIFFRACTION100
3.981-4.16210.26011350.21121865X-RAY DIFFRACTION100
4.1621-4.38130.26041450.20051856X-RAY DIFFRACTION100
4.3813-4.65560.26341470.19841836X-RAY DIFFRACTION100
4.6556-5.01460.24831320.20791886X-RAY DIFFRACTION100
5.0146-5.51850.27281510.22651856X-RAY DIFFRACTION100
5.5185-6.31510.29751440.25481883X-RAY DIFFRACTION100
6.3151-7.94930.29611440.24641890X-RAY DIFFRACTION100
7.9493-45.11560.26751460.21221935X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 40.94 Å / Origin y: 48.2468 Å / Origin z: 40.8901 Å
111213212223313233
T0.4884 Å2-0.0768 Å20.0363 Å2-0.4267 Å2-0.026 Å2--0.3415 Å2
L0.4262 °20.0865 °20.1937 °2-0.6441 °20.2054 °2--0.2053 °2
S-0.042 Å °-0.0077 Å °0.1038 Å °-0.1124 Å °0.1011 Å °-0.1759 Å °0.1267 Å °0.0384 Å °0.0794 Å °
Refinement TLS groupSelection details: all

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