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- PDB-6ivh: Crystal structure of the N-terminal domain of ScpA derived from T... -

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Basic information

Entry
Database: PDB / ID: 6ivh
TitleCrystal structure of the N-terminal domain of ScpA derived from Thermococcus onnurineus
ComponentsSegregation and condensation protein A
KeywordsCELL CYCLE / CYTOSOLIC PROTEIN / Condensin / kleisin
Function / homologySegregation and condensation protein A / Segregation and condensation protein ScpA / ScpA-like, C-terminal / Segregation and condensation protein A
Function and homology information
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJeon, J.-H. / Shin, H.-C. / 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
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segregation and condensation protein A


Theoretical massNumber of molelcules
Total (without water)15,1621
Polymers15,1621
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6110 Å2
Unit cell
Length a, b, c (Å)76.984, 76.984, 39.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Segregation and condensation protein A


Mass: 15161.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_1071 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6YWU6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: crystal growth at 3.5 M sodium formate and 0.1 M sodium malonate, dehydration for 2 h in the reservoir solution containing additional 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8911 / % possible obs: 97.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 40.12 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.028 / Rrim(I) all: 0.084 / Χ2: 2.338 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5430.2794120.3270.1590.3240.93489.6
2.54-2.593.30.2783940.3170.1620.3250.92591.2
2.59-2.643.40.2794520.4030.1570.3230.88992.6
2.64-2.6940.2494080.7630.1220.281.17392.7
2.69-2.754.20.2754310.6670.1360.3091.23194.3
2.75-2.824.50.244370.8460.1140.2681.23896.5
2.82-2.894.70.2274510.8260.1060.2521.12994.9
2.89-2.964.90.2164440.8780.0990.2391.23197.4
2.96-3.055.80.1964610.9280.0840.2141.26299.1
3.05-3.156.10.1714420.9610.070.1861.44299.8
3.15-3.266.80.1384520.9840.0540.1481.68198.7
3.26-3.397.30.1174640.9850.0440.1251.799.4
3.39-3.558.20.0994560.9910.0360.1062.161100
3.55-3.738.50.0974350.9920.0340.1032.19199.8
3.73-3.978.90.0874870.9960.030.0922.85899.8
3.97-4.279.40.0744530.9970.0250.0783.33599.8
4.27-4.79.60.0664400.9970.0220.073.30199.8
4.7-5.389.80.0644740.9980.0210.0673.22100
5.38-6.789.50.0694580.9970.0230.0733.054100
6.78-5010.80.0544600.9990.0170.0563.62899.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→38.492 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.75 / Phase error: 25.14
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2589 882 9.91 %
Rwork0.2391 --
obs0.2416 8904 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.83 Å2 / Biso mean: 53.5061 Å2 / Biso min: 24.4 Å2
Refinement stepCycle: final / Resolution: 2.5→38.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 0 1 769
Biso mean---37.29 -
Num. residues----94
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004776
X-RAY DIFFRACTIONf_angle_d0.7321047
X-RAY DIFFRACTIONf_chiral_restr0.046126
X-RAY DIFFRACTIONf_plane_restr0.002131
X-RAY DIFFRACTIONf_dihedral_angle_d19.185489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.65670.34411280.3081256138491
2.6567-2.86170.33221490.27681302145195
2.8617-3.14960.28561390.26531357149698
3.1496-3.60510.30181550.23481377153299
3.6051-4.54080.23031620.20513631525100
4.5408-38.49650.211490.231713671516100

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