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- PDB-4i98: Crystal structure of the complex between ScpA(residues 1-160)-Scp... -

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Basic information

Entry
Database: PDB / ID: 4i98
TitleCrystal structure of the complex between ScpA(residues 1-160)-ScpB(residues 1-183)
Components
  • Segregation and condensation protein A
  • Segregation and condensation protein B
KeywordsCELL CYCLE / ScpA / ScpB / DNA condensation / SMC
Function / homology
Function and homology information


chromosome separation / chromosome segregation / DNA replication / cell cycle / 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 / 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 / Segregation and condensation protein A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsShin, H.C. / Oh, B.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: An asymmetric SMC-kleisin bridge in prokaryotic condensin
Authors: Burmann, F. / Shin, H.C. / Basquin, J. / Soh, Y.M. / Gimenez-Oya, V. / Kim, Y.G. / Oh, B.H. / Gruber, S.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Experimental preparation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segregation and condensation protein A
B: Segregation and condensation protein B
C: Segregation and condensation protein B


Theoretical massNumber of molelcules
Total (without water)59,7493
Polymers59,7493
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-77 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.297, 82.720, 59.909
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Segregation and condensation protein A


Mass: 18932.826 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: P1031 / Gene: scpA, SPP_1876 / Plasmid: pCDF Duet / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: C1CMI6
#2: Protein Segregation and condensation protein B


Mass: 20408.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: P1031 / Gene: scpB, SPP_1875 / Plasmid: pCDF Duet / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: C1CMI5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.8 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200mM trimethylamine N-oxide, 100mM Tris-HCl, 20% polyethylene glycol monomethyl ether 2000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 22286 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 42.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.79 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→39.27 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.259 927
Rwork0.24 -
all-22190
obs-19082
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a1.06 Å1.09 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 0 4 3769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048
RfactorNum. reflection% reflection
Rfree0.521 120 -
Rwork0.488 --
obs-2293 65.4 %

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