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- PDB-4rsj: Pyrococcus furiosus Smc hinge domain with an extended coiled coil -

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Basic information

Entry
Database: PDB / ID: 4rsj
TitlePyrococcus furiosus Smc hinge domain with an extended coiled coil
ComponentsChromosome partition protein Smc
KeywordsCELL CYCLE / Smc hinge domain with coiled coils
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome segregation / chromosome / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Structural maintenance of chromosomes protein, prokaryotic / 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
Chromosome partition protein Smc
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSoh, Y.M. / Shin, H.C. / Oh, B.H.
CitationJournal: Mol.Cell / Year: 2015
Title: Molecular Basis for SMC Rod Formation and Its Dissolution upon DNA Binding.
Authors: Soh, Y.M. / Burmann, F. / Shin, H.C. / Oda, T. / Jin, K.S. / Toseland, C.P. / Kim, C. / Lee, H. / Kim, S.J. / Kong, M.S. / Durand-Diebold, M.L. / Kim, Y.G. / Kim, H.M. / Lee, N.K. / Sato, M. ...Authors: Soh, Y.M. / Burmann, F. / Shin, H.C. / Oda, T. / Jin, K.S. / Toseland, C.P. / Kim, C. / Lee, H. / Kim, S.J. / Kong, M.S. / Durand-Diebold, M.L. / Kim, Y.G. / Kim, H.M. / Lee, N.K. / Sato, M. / Oh, B.H. / Gruber, S.
History
DepositionNov 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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: Chromosome partition protein Smc
B: Chromosome partition protein Smc
C: Chromosome partition protein Smc
D: Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)123,4414
Polymers123,4414
Non-polymers00
Water00
1
A: Chromosome partition protein Smc
B: Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)61,7212
Polymers61,7212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-21 kcal/mol
Surface area28940 Å2
MethodPISA
2
C: Chromosome partition protein Smc
D: Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)61,7212
Polymers61,7212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-20 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.923, 116.882, 145.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chromosome partition protein Smc


Mass: 30860.355 Da / Num. of mol.: 4 / Fragment: Smc hinge
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: smc, PF1843 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q8TZY2

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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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1 M Sodium Citrate, 0.1 M CHES pH 9.5, 8% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 20012 / Num. obs: 18608 / % possible obs: 89.5 % / Rsym value: 0.093 / Net I/σ(I): 26.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAutoMRmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NWC

3nwc


Resolution: 3.5→50 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.284 928 5% random
Rwork0.236 --
all-20012 -
obs-18608 -
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7715 0 0 0 7715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.78

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