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- PDB-3w6k: Crystal structure of dimer of ScpB N-terminal domain complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3w6k
TitleCrystal structure of dimer of ScpB N-terminal domain complexed with ScpA peptide
Components
  • ScpA
  • ScpB
KeywordsCELL CYCLE / regulatory subcomplex / SMC / winged HTH
Function / homology
Function and homology information


chromosome separation / DNA replication / cell division / cytoplasm
Similarity search - Function
Chromosome segregation/condensation protein ScpB / Segregation and condensation complex subunit ScpB / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Segregation and condensation protein B
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.374 Å
AuthorsKamada, K. / Hirano, T.
CitationJournal: Structure / Year: 2013
Title: Molecular basis of SMC ATPase activation: role of internal structural changes of the regulatory subcomplex ScpAB
Authors: Kamada, K. / Miyata, M. / Hirano, T.
History
DepositionFeb 15, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ScpA
B: ScpB
C: ScpB
D: ScpA
E: ScpB
F: ScpB


Theoretical massNumber of molelcules
Total (without water)43,0386
Polymers43,0386
Non-polymers00
Water1,820101
1
A: ScpA
B: ScpB
C: ScpB


Theoretical massNumber of molelcules
Total (without water)21,5193
Polymers21,5193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-42 kcal/mol
Surface area9370 Å2
MethodPISA
2
D: ScpA
E: ScpB
F: ScpB


Theoretical massNumber of molelcules
Total (without water)21,5193
Polymers21,5193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-34 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.823, 88.919, 60.683
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide ScpA


Mass: 1996.222 Da / Num. of mol.: 2 / Fragment: UNP residues 125-142 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Geobacillus stearothermophilus (bacteria) / References: UniProt: A0A0E0TE00*PLUS
#2: Protein
ScpB


Mass: 9761.276 Da / Num. of mol.: 4 / Fragment: UNp residues 12-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: strain 10 / Gene: scpB / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E0TE00*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN ENTITY 2, GPHM HAVE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN ENTITY 2, GPHM HAVE BEEN ADDED AT N-TERMINAL.

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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: 63.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100mM Na malonate-HCl, 3.0-3.3M Na formate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 2.374→50 Å / Num. obs: 23087 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.586 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 37.406
Reflection shellResolution: 2.374→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 11.464 / Num. unique all: 1048 / Rsym value: 0.116 / % possible all: 89.8

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dimer of Geobacillus stearothermophilus ScpB N-terminal domain

Resolution: 2.374→46.476 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 1182 5.13 %RANDOM
Rwork0.2358 ---
obs0.2383 23058 99.42 %-
all-23191 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.526 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7307 Å20 Å21.3997 Å2
2---4.2974 Å2-0 Å2
3----2.4333 Å2
Refinement stepCycle: LAST / Resolution: 2.374→46.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 0 101 2860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092786
X-RAY DIFFRACTIONf_angle_d1.2963749
X-RAY DIFFRACTIONf_dihedral_angle_d15.5781058
X-RAY DIFFRACTIONf_chiral_restr0.073451
X-RAY DIFFRACTIONf_plane_restr0.008479
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.374-2.48180.41161280.28692682281097
2.4818-2.61270.29621490.254227082857100
2.6127-2.77630.29531370.233727562895100
2.7763-2.99070.30091500.247527352885100
2.9907-3.29150.27671590.250427112870100
3.2915-3.76770.29761630.230527332896100
3.7677-4.74610.28771510.208127552906100
4.7461-46.48470.23611450.239727962941100

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