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- PDB-5h69: Crystal structure of an asymmetric dimer of the Geobacillus stear... -

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Basic information

Entry
Database: PDB / ID: 5h69
TitleCrystal structure of an asymmetric dimer of the Geobacillus stearothermophilus SMC hinge domain
ComponentsChromosome partition protein Smc
KeywordsDNA BINDING PROTEIN / CELL CYCLE / SMC protein
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome / DNA replication / 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 speciesGeobacillus stearothermophilus 10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20040022156 Å
AuthorsKamada, K. / Hirano, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Grants-in-Aid for Science Research Japan
CitationJournal: Structure / Year: 2017
Title: Overall Shapes of the SMC-ScpAB Complex Are Determined by Balance between Constraint and Relaxation of Its Structural Parts
Authors: Kamada, K. / Su'etsugu, M. / Takada, H. / Miyata, M. / Hirano, T.
History
DepositionNov 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 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
B: Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)57,9342
Polymers57,9342
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-10 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.144, 77.144, 114.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Chromosome partition protein Smc


Mass: 28967.014 Da / Num. of mol.: 2 / Fragment: UNP residues 463-719
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus 10 (bacteria)
Gene: smc, GT50_02560 / Plasmid: pET-28m / Details (production host): modified / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0K2H586
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.08 Å3/Da / Density % sol: 60.07 % / Description: Needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M magnesium formate, 15%(w/v) PEG 33500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2012
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34064 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 30.89 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 46.9 / Net I/σ(I): 18
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.214 / Rsym value: 0.214 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GXJ

1gxj


Resolution: 2.20040022156→36.5631717256 Å / SU ML: 0.226772278776 / Cross valid method: FREE R-VALUE / σ(F): 1.38098488499 / Phase error: 24.9111737956
RfactorNum. reflection% reflection
Rfree0.240738181013 1724 5.06656478679 %
Rwork0.193277072277 --
obs0.195743440621 34027 99.9706202074 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.5138348812 Å2
Refinement stepCycle: LAST / Resolution: 2.20040022156→36.5631717256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 0 172 4069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722016804543956
X-RAY DIFFRACTIONf_angle_d0.8462714521995335
X-RAY DIFFRACTIONf_chiral_restr0.0476937703474598
X-RAY DIFFRACTIONf_plane_restr0.00465918114065700
X-RAY DIFFRACTIONf_dihedral_angle_d4.786019059842415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.26510.2473684325861410.1822069809912701X-RAY DIFFRACTION100
2.2651-2.33820.2434476035841340.2008331488142665X-RAY DIFFRACTION100
2.3382-2.42180.2703929440341570.2051339271432661X-RAY DIFFRACTION100
2.4218-2.51870.2682285110611400.2083081669342697X-RAY DIFFRACTION100
2.5187-2.63330.2678773531051250.2170245426522693X-RAY DIFFRACTION99.9645264278
2.6333-2.77210.2795795342841340.2219038353322700X-RAY DIFFRACTION100
2.7721-2.94570.3213234741841410.2261466453462686X-RAY DIFFRACTION100
2.9457-3.17310.2880057219211510.2243299083132683X-RAY DIFFRACTION100
3.1731-3.49220.2513589268151470.215120075042703X-RAY DIFFRACTION99.9649245879
3.4922-3.99690.2177892578441580.1885827574412663X-RAY DIFFRACTION100
3.9969-5.03360.1883034030351450.1584209565112712X-RAY DIFFRACTION100
5.0336-36.56820.2166945641841510.1650741840142739X-RAY DIFFRACTION99.72394755

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