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- PDB-6qj2: Crystal structure of the C. thermophilum condensin Smc4 ATPase he... -

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Basic information

Entry
Database: PDB / ID: 6qj2
TitleCrystal structure of the C. thermophilum condensin Smc4 ATPase head in complex with the C-terminal domain of Brn1
Components
  • Condensin complex subunit 2
  • Smc4
KeywordsCELL CYCLE / condensin / SMC complex / ATPase / chromosome condensation / loop extrusion
Function / homology
Function and homology information


condensin complex / mitotic chromosome condensation / chromosome organization / chromosome / cell division / regulation of DNA-templated transcription / DNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / Condensin complex subunit 2/barren / Condensin complex subunit 2 / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / DNA binding domain with preference for A/T rich regions / RecF/RecN/SMC, N-terminal ...HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / Condensin complex subunit 2/barren / Condensin complex subunit 2 / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / DNA binding domain with preference for A/T rich regions / RecF/RecN/SMC, N-terminal / AT hook, DNA-binding motif / RecF/RecN/SMC N terminal domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SMC hinge domain-containing protein / Condensin complex subunit 2
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Smc4
B: Condensin complex subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6838
Polymers60,1072
Non-polymers5766
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-93 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.728, 132.728, 75.548
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Smc4


Mass: 44726.895 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_0017120 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0S2G2
#2: Protein Condensin complex subunit 2


Mass: 15380.184 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 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G0SBJ6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

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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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3 % (v/v) EtOH, 0.1 M Na citrate pH 6.0, 1.5 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→114.946 Å / Num. obs: 16953 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Rsym value: 0.086 / Net I/av σ(I): 4.1 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.067.11.4970.524540.6011.6141.49799.7
3.06-3.246.90.758123440.3120.820.75899.9
3.24-3.476.80.3342.321670.1370.3620.33499.8
3.47-3.747.10.174.320310.0680.1830.17100
3.74-4.16.70.1036.718950.0430.1120.10399.9
4.1-4.597.10.0768.117070.0310.0820.076100
4.59-5.296.80.0668.915120.0270.0720.066100
5.29-6.486.90.067912690.0270.0720.06799.8
6.48-9.176.60.0618.810060.0250.0660.06199.9
9.17-45.7416.40.0629.15680.0260.0680.06299

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W1W

1w1w


Resolution: 3→43.445 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.99
RfactorNum. reflection% reflection
Rfree0.243 766 5 %
Rwork0.2138 --
obs0.2153 15305 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 316.08 Å2 / Biso mean: 125.0163 Å2 / Biso min: 55.86 Å2
Refinement stepCycle: final / Resolution: 3→43.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 30 0 3504
Biso mean--172.35 --
Num. residues----441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0002-3.23180.341460.299228873033
3.2318-3.55690.33411610.260428813042
3.5569-4.07130.26251610.222828743035
4.0713-5.12810.21511470.184629323079
5.1281-43.450.22271510.208829653116
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)
12.0970.1260.30044.50131.2266.2397-0.15630.16970.31530.20510.05480.0858-0.4598-0.04890.11020.56750.05350.00480.663-0.0060.751844.620446.037627.2849
22.73251.18491.85023.18840.94282.7732-0.182-0.37080.21360.5618-0.21550.10420.08270.01590.34020.86040.0562-0.06740.7776-0.11250.808951.538444.362344.9653
34.45080.54440.42825.75630.86464.20570.5771-0.2958-0.93020.47350.1268-0.13062.1566-0.0503-0.50161.80550.0565-0.18840.75380.0150.979146.709313.952531.9001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 270 through 460)A270 - 460
2X-RAY DIFFRACTION2chain 'A' and (resid 1376 through 1539 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 771 through 893 )B771 - 893

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