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- PDB-5xns: Crystal structure of the Smc head domain with an extended coiled ... -

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Basic information

Entry
Database: PDB / ID: 5xns
TitleCrystal structure of the Smc head domain with an extended coiled coil bound to the C-terminal domain of ScpA derived from Pyrococcus furiosus
Components
  • Chromosome partition protein Smc
  • Segregation and condensation protein A
KeywordsDNA BINDING PROTEIN/CELL CYCLE / Condensin / Smc / head domain / ScpA / DNA BINDING PROTEIN-CELL CYCLE complex
Function / homology
Function and homology information


cohesin loader activity / chromosome condensation / mitotic sister chromatid cohesion / chromosome segregation / chromosome / double-stranded DNA binding / DNA replication / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Structural maintenance of chromosome 1. Chain E / Segregation and condensation protein A / Segregation and condensation protein ScpA / Structural maintenance of chromosomes protein, prokaryotic / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain ...Structural maintenance of chromosome 1. Chain E / Segregation and condensation protein A / Segregation and condensation protein ScpA / Structural maintenance of chromosomes protein, prokaryotic / ScpA-like, C-terminal / 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 / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Chromosome partition protein Smc / Segregation/condensation protein A
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKwak, M.-J. / Shin, H.-C. / Oh, B.-H.
CitationJournal: Mol. Cell / Year: 2017
Title: Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization
Authors: Diebold-Durand, M.L. / Lee, H. / Ruiz Avila, L.B. / Noh, H. / Shin, H.-C. / Im, H. / Bock, F.P. / Burmann, F. / Durand, A. / Basfeld, A. / Ham, S. / Basquin, J. / Oh, B.-H. / Gruber, S.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Chromosome partition protein Smc
C: Segregation and condensation protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3884
Polymers54,0032
Non-polymers3842
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-22 kcal/mol
Surface area22760 Å2
MethodPISA
2
A: Chromosome partition protein Smc
C: Segregation and condensation protein A
hetero molecules

A: Chromosome partition protein Smc
C: Segregation and condensation protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7758
Polymers108,0074
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9280 Å2
ΔGint-60 kcal/mol
Surface area42930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.304, 150.003, 51.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Chromosome partition protein Smc


Mass: 45220.027 Da / Num. of mol.: 1
Fragment: UNP residues 1-201 and 973-1069, linked with linker residues SGGSGGS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: smc, PF1843 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZY2
#2: Protein Segregation and condensation protein A


Mass: 8783.374 Da / Num. of mol.: 1 / Fragment: UNP residues 143-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1842 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZY3
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1M Ammonium citrate dibasic, 0.1M Sodium acetate trihydrate pH 4.6, 0.3M NDSB-195

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 45242 / % possible obs: 92.8 % / Redundancy: 6 % / Biso Wilson estimate: 27.06 Å2 / Net I/σ(I): 31.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MR-Rosettaphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I99

4i99


Resolution: 2.01→42.932 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.66 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.2369 2000 4.42 %
Rwork0.2068 --
obs0.2082 45214 92.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.73 Å2 / Biso mean: 34.2864 Å2 / Biso min: 13.78 Å2
Refinement stepCycle: final / Resolution: 2.01→42.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 26 32 3790
Biso mean--44.31 31.32 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083816
X-RAY DIFFRACTIONf_angle_d0.9575126
X-RAY DIFFRACTIONf_chiral_restr0.052569
X-RAY DIFFRACTIONf_plane_restr0.005659
X-RAY DIFFRACTIONf_dihedral_angle_d17.8562367
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0097-2.05990.3941920.34251987207960
2.0599-2.11560.32041310.29572816294787
2.1156-2.17790.31361340.25762924305890
2.1779-2.24810.28081410.25353017315892
2.2481-2.32850.28391410.22823074321593
2.3285-2.42170.26161420.22453050319293
2.4217-2.53190.27211460.21453149329596
2.5319-2.66540.26671470.22323186333396
2.6654-2.83240.28291510.2233251340298
2.8324-3.0510.21871500.22463250340099
3.051-3.35790.23971520.22263289344199
3.3579-3.84350.21961540.18623346350099
3.8435-4.84140.17751570.16383362351999
4.8414-42.94130.20061620.17423513367599

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