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- PDB-5h67: Crystal structure of the Bacillus subtilis SMC head domain comple... -

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Basic information

Entry
Database: PDB / ID: 5h67
TitleCrystal structure of the Bacillus subtilis SMC head domain complexed with the cognate ScpA C-terminal domain and soaked ATP
Components
  • (Chromosome partition protein Smc) x 2
  • Segregation and condensation protein A
KeywordsDNA BINDING PROTEIN/CELL CYCLE / SMC protein / DNA BINDING PROTEIN-CELL CYCLE complex
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome segregation / chromosome / DNA replication / cell division / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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 ...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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Segregation and condensation protein A / Chromosome partition protein Smc
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07203506543 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,7814
Polymers53,2743
Non-polymers5071
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-70 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.009, 47.124, 97.698
Angle α, β, γ (deg.)90.000, 112.594, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Chromosome partition protein Smc


Mass: 22517.609 Da / Num. of mol.: 1 / Fragment: N-terminal, UNP residues 1-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: smc, ylqA, BSU15940 / Plasmid: pET-22b / Details (production host): coexpression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51834
#2: Protein Chromosome partition protein Smc


Mass: 21466.559 Da / Num. of mol.: 1 / Fragment: C-terminal, UNP residues 1000-1186 / Mutation: E1118Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: smc, ylqA, BSU15940 / Plasmid: pET-22b / Details (production host): coexpression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51834
#3: Protein Segregation and condensation protein A


Mass: 9289.652 Da / Num. of mol.: 1 / Fragment: UNP residues 176-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: scpA, ypuG, BSU23220 / Plasmid: pET-28m / Details (production host): modified / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35154
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.67 Å3/Da / Density % sol: 66.46 % / Description: Orthogonal plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 3.5M sodium formate (pH 7.4), the crystals were soaked in the reservoir solution containing 10mM Mg-ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / 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: 2.07→50 Å / Num. obs: 44563 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 32.0993476008 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/av σ(I): 27.5 / Net I/σ(I): 14.8
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.244 / Rsym value: 0.244 / % possible all: 86.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H66

5h66


Resolution: 2.07203506543→40.627174663 Å / SU ML: 0.199736653153 / Cross valid method: FREE R-VALUE / σ(F): 1.36326163552 / Phase error: 22.5281067016
RfactorNum. reflection% reflection
Rfree0.222032699053 2253 5.05780671231 %
Rwork0.190725701584 --
obs0.192361109808 44545 97.9592285532 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.2498877626 Å2
Refinement stepCycle: LAST / Resolution: 2.07203506543→40.627174663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 31 183 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008144943273453727
X-RAY DIFFRACTIONf_angle_d0.847622515855017
X-RAY DIFFRACTIONf_chiral_restr0.0532537812128564
X-RAY DIFFRACTIONf_plane_restr0.00457731953232647
X-RAY DIFFRACTIONf_dihedral_angle_d3.056207180852654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.072-2.11710.2751501153511190.2196747394282160X-RAY DIFFRACTION81.596849266
2.1171-2.16630.2274254847761470.1950116712062526X-RAY DIFFRACTION94.6865037194
2.1663-2.22050.2243931796281240.1968750359782648X-RAY DIFFRACTION97.9505300353
2.2205-2.28050.2454856256291400.198181381532627X-RAY DIFFRACTION98.9274222381
2.2805-2.34760.2260249167611260.2058867116612684X-RAY DIFFRACTION99.1531404375
2.3476-2.42340.233957912791310.1955184930682652X-RAY DIFFRACTION99.428367274
2.4234-2.510.2415664987051330.19715191472695X-RAY DIFFRACTION99.5424146427
2.51-2.61050.2285981653571430.2022512407582685X-RAY DIFFRACTION99.6476391825
2.6105-2.72930.2289724188421560.1987397353932641X-RAY DIFFRACTION99.5728017088
2.7293-2.87310.2812351038831300.212051413692712X-RAY DIFFRACTION99.6144409394
2.8731-3.05310.2785885097511440.208069045162683X-RAY DIFFRACTION99.7529992943
3.0531-3.28870.224478295531470.199762467662673X-RAY DIFFRACTION99.6818663839
3.2887-3.61950.2228506428551550.1920759435882710X-RAY DIFFRACTION99.9651081647
3.6195-4.14280.2140293855161570.1816065688112702X-RAY DIFFRACTION99.7905759162
4.1428-5.21770.1728447601221610.1668339441992731X-RAY DIFFRACTION99.7585374267
5.2177-40.6350.2217265026841400.184302473372763X-RAY DIFFRACTION98.0081026334

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