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- PDB-3w6j: Crystal structure of ScpAB core complex -

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Basic information

Entry
Database: PDB / ID: 3w6j
TitleCrystal structure of ScpAB core complex
Components
  • ScpA
  • ScpB
KeywordsCELL CYCLE / regulatory subcomplex / SMC / winged HTH
Function / homology
Function and homology information


chromosome separation / chromosome segregation / DNA replication / cell division / cytoplasm
Similarity search - Function
Chromosome segregation/condensation protein ScpB / Segregation and condensation complex subunit ScpB / Segregation and condensation protein A / Segregation and condensation protein ScpA / ScpA-like, C-terminal / 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 A / Segregation and condensation protein B
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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

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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)120,4326
Polymers120,4326
Non-polymers00
Water77543
1
A: ScpA
B: ScpB
C: ScpB


Theoretical massNumber of molelcules
Total (without water)60,2163
Polymers60,2163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-78 kcal/mol
Surface area24320 Å2
MethodPISA
2
D: ScpA
E: ScpB
F: ScpB


Theoretical massNumber of molelcules
Total (without water)60,2163
Polymers60,2163
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-81 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.856, 127.423, 97.218
Angle α, β, γ (deg.)90.00, 113.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ScpA


Mass: 20138.232 Da / Num. of mol.: 2 / Fragment: Unp residues 1-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: strain 10 / Gene: scpA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E0TD69*PLUS
#2: Protein
ScpB


Mass: 20038.943 Da / Num. of mol.: 4 / Fragment: UNP resides 12-191 / Mutation: extra a.a. GPHM at Nter
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) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E0TE00*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. In THE ENTITY 2, GPHM ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. In THE ENTITY 2, GPHM AMINO ACIDS HAVE BEEN ADDED AT THE 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: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.49M NaH2PO4, 0.91M K2HPO4, pH 7.2, VAPOR DIFFUSION, SITTING 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: Jul 14, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 61981 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 66.659 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19.793
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.625 / Num. unique all: 5598 / Rsym value: 0.669 / % possible all: 89.5

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→30.7 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 3144 5.07 %RANDOM
Rwork0.2247 ---
obs0.2267 61951 98.69 %-
all-61972 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.228 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.6874 Å2-0 Å29.8465 Å2
2---16.2021 Å2-0 Å2
3---1.5148 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7499 0 0 43 7542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097623
X-RAY DIFFRACTIONf_angle_d1.18110305
X-RAY DIFFRACTIONf_dihedral_angle_d15.472972
X-RAY DIFFRACTIONf_chiral_restr0.0721203
X-RAY DIFFRACTIONf_plane_restr0.0051322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6-2.6330.43821190.36432204232381
2.633-2.67610.34591430.33582632277598
2.6761-2.72220.40651310.32762676280799
2.7222-2.77170.37141660.31322681284799
2.7717-2.8250.3371320.30042676280899
2.825-2.88260.31591390.277826682807100
2.8826-2.94520.35461470.28662693284099
2.9452-3.01370.29651270.27732706283399
3.0137-3.0890.28711520.27072654280699
3.089-3.17240.31751440.26452698284299
3.1724-3.26570.34331530.26542696284999
3.2657-3.37090.27891400.237726842824100
3.3709-3.49130.28161510.232226942845100
3.4913-3.63080.24081350.217827242859100
3.6308-3.79580.2421410.21626732814100
3.7958-3.99550.22771410.197727062847100
3.9955-4.24530.23391310.183127312862100
4.2453-4.57210.22971610.177227002861100
4.5721-5.03040.21661310.191427152846100
5.0304-5.75410.2981590.231127242873100
5.7541-7.23390.2811420.245927232865100
7.2339-30.70260.19391590.17682749290899

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