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- PDB-5h66: Crystal structure of the Bacillus subtilis SMC head domain comple... -

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Basic information

Entry
Database: PDB / ID: 5h66
TitleCrystal structure of the Bacillus subtilis SMC head domain complexed with the cognate ScpA C-terminal domain
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
Segregation and condensation protein A / Chromosome partition protein Smc
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82194772804 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


Theoretical massNumber of molelcules
Total (without water)53,2743
Polymers53,2743
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-70 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.151, 46.905, 97.194
Angle α, β, γ (deg.)90.000, 112.650, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.73 Å3/Da / Density % sol: 67.03 % / Description: Orthogonal plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 3.5M sodium formate (pH 7.4)

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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: 1.82→50 Å / Num. obs: 65862 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 23.509975769 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/av σ(I): 30.2 / Net I/σ(I): 14.1
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.258 / Rsym value: 0.258 / % possible all: 99.4

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Processing

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

1xew


Resolution: 1.82194772804→34.5967717027 Å / SU ML: 0.18789881426 / Cross valid method: FREE R-VALUE / σ(F): 1.33778337783 / Phase error: 23.7348302365
RfactorNum. reflection% reflection
Rfree0.227528161967 3341 5.07380634188 %
Rwork0.210874153035 --
obs0.211745635755 65848 99.6338326524 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.5291876369 Å2
Refinement stepCycle: LAST / Resolution: 1.82194772804→34.5967717027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 143 3638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675993826563548
X-RAY DIFFRACTIONf_angle_d0.7350591914794771
X-RAY DIFFRACTIONf_chiral_restr0.0499542832722542
X-RAY DIFFRACTIONf_plane_restr0.00390393381457618
X-RAY DIFFRACTIONf_dihedral_angle_d2.607647350492169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8219-1.8480.3199519234861200.2670103915682447X-RAY DIFFRACTION94.9334319527
1.848-1.87560.2766781644951440.2446168458562623X-RAY DIFFRACTION99.6040316775
1.8756-1.90490.2232746231191410.2277821410642566X-RAY DIFFRACTION100
1.9049-1.93610.2199823760111380.2180296730482595X-RAY DIFFRACTION99.9634235552
1.9361-1.96950.2428249436021530.2070590978512568X-RAY DIFFRACTION99.9265515975
1.9695-2.00530.2114848804241310.2074762015432609X-RAY DIFFRACTION100
2.0053-2.04380.215788539131490.2019415948232615X-RAY DIFFRACTION99.9638336347
2.0438-2.08560.2495317460081330.2059559294472553X-RAY DIFFRACTION100
2.0856-2.13090.2357892098951410.2091596313452623X-RAY DIFFRACTION99.9638336347
2.1309-2.18050.2263341822311470.2050696663352583X-RAY DIFFRACTION100
2.1805-2.2350.25188400861150.2029975271982629X-RAY DIFFRACTION100
2.235-2.29540.2132017490591520.2093083744412575X-RAY DIFFRACTION100
2.2954-2.36290.2294404455521210.2184031344892621X-RAY DIFFRACTION100
2.3629-2.43920.2629920874541270.2198589583992632X-RAY DIFFRACTION100
2.4392-2.52630.2440414694491330.2301931012462602X-RAY DIFFRACTION100
2.5263-2.62740.2586691926741460.2323309722082617X-RAY DIFFRACTION100
2.6274-2.7470.2372514471841330.2250845211152609X-RAY DIFFRACTION99.9271137026
2.747-2.89170.3164713309821380.2419909451942612X-RAY DIFFRACTION100
2.8917-3.07280.2515036577391440.2313102923342619X-RAY DIFFRACTION99.9638205499
3.0728-3.30990.2357417449041390.2347579937322626X-RAY DIFFRACTION99.9277195519
3.3099-3.64270.255183337011480.2103815052882618X-RAY DIFFRACTION99.8555956679
3.6427-4.1690.17825248061640.1986862534662622X-RAY DIFFRACTION99.820852741
4.169-5.24950.1661287291510.1722271217122632X-RAY DIFFRACTION99.4994637111
5.2495-34.6030.2326007268151330.193605081322711X-RAY DIFFRACTION97.900172117

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