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- PDB-6juv: Crytsal structure of ScpB derived from Pyrococcus yayanosii -

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Basic information

Entry
Database: PDB / ID: 6juv
TitleCrytsal structure of ScpB derived from Pyrococcus yayanosii
ComponentsSegregation and condensation protein B
KeywordsCELL CYCLE / cytosolic protein / condensin / kite
Function / homologyChromosome segregation/condensation protein ScpB / Segregation and condensation complex subunit ScpB / chromosome separation / Winged helix DNA-binding domain superfamily / cell division / Winged helix-like DNA-binding domain superfamily / Segregation and condensation protein B
Function and homology information
Biological speciesPyrococcus yayanosii CH1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.043 Å
AuthorsJeon, J.-H. / Lee, H. / Oh, B.-H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2018R1A2B3004764 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Archaeal Smc-based condensin lacking kite subunits
Authors: Jeon, J.-H. / Lee, H.-S. / Shin, H.-C. / Kwak, M.-J. / Kim, Y.-K. / Gruber, S. / Oh, B.-H.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segregation and condensation protein B
B: Segregation and condensation protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6893
Polymers45,6542
Non-polymers351
Water1629
1
A: Segregation and condensation protein B

A: Segregation and condensation protein B


Theoretical massNumber of molelcules
Total (without water)45,6542
Polymers45,6542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area3490 Å2
ΔGint-26 kcal/mol
Surface area21370 Å2
MethodPISA
2
B: Segregation and condensation protein B
hetero molecules

B: Segregation and condensation protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7254
Polymers45,6542
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area3620 Å2
ΔGint-39 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.300, 92.300, 111.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Segregation and condensation protein B


Mass: 22826.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus yayanosii CH1 (archaea) / Gene: PYCH_12850 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8AFC4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 0.1M MES (pH 5.5), 0.4M sodium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 5C (4A)10.9794
SYNCHROTRONPAL/PLS 11C20.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJul 24, 2018
DECTRIS PILATUS3 6M2PIXELOct 22, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97941
ReflectionResolution: 3.04→92.3 Å / Num. obs: 9802 / % possible obs: 100 % / Redundancy: 113.1 % / Biso Wilson estimate: 67.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.017 / Rrim(I) all: 0.172 / Χ2: 0.91 / Net I/av σ(I): 34.3 / Net I/σ(I): 34.3
Reflection shellResolution: 3.04→3.25 Å / Redundancy: 118.9 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 20.2 / Num. unique obs: 1721 / CC1/2: 0.998 / Rpim(I) all: 0.035 / Rrim(I) all: 0.387 / Χ2: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: SAD / Resolution: 3.043→92.3 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.87
RfactorNum. reflection% reflection
Rfree0.2649 978 10.01 %
Rwork0.2357 --
obs0.2387 9775 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.05 Å2 / Biso mean: 58.3248 Å2 / Biso min: 13.72 Å2
Refinement stepCycle: final / Resolution: 3.043→92.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 1 9 2966
Biso mean--68.96 36.91 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023004
X-RAY DIFFRACTIONf_angle_d0.4954051
X-RAY DIFFRACTIONf_chiral_restr0.035469
X-RAY DIFFRACTIONf_plane_restr0.003508
X-RAY DIFFRACTIONf_dihedral_angle_d15.8751865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0434-3.20380.37131360.310212221358
3.2038-3.40460.34891350.283512201355
3.4046-3.66740.29931380.261812371375
3.6674-4.03650.25491370.231412351372
4.0365-4.62060.2471380.214412501388
4.6206-5.82130.25181420.22112681410
5.8213-92.34230.23131520.219313651517

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