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- PDB-5xg2: Crystal structure of a coiled-coil segment (residues 345-468 and ... -

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Basic information

Entry
Database: PDB / ID: 5xg2
TitleCrystal structure of a coiled-coil segment (residues 345-468 and 694-814) of Pyrococcus yayanosii Smc
ComponentsChromosome partition protein Smc
KeywordsDNA BINDING PROTEIN / Smc / coiled-coil / Prokaryotic condensin
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Structural maintenance of chromosomes protein, prokaryotic / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromosome partition protein Smc
Similarity search - Component
Biological speciesPyrococcus yayanosii
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNoh, H. / Lee, H. / Oh, B.-H.
CitationJournal: Mol. Cell / Year: 2017
Title: Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization
Authors: Diebold-Durand, M.L. / Lee, H. / Ruiz Avila, L.B. / Noh, H. / Shin, H.C. / Im, H. / Bock, F.P. / Burmann, F. / Durand, A. / Basfeld, A. / Ham, S. / Basquin, J. / Oh, B.-H. / Gruber, S.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosome partition protein Smc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7055
Polymers30,2331
Non-polymers4734
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-17 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.175, 53.710, 71.399
Angle α, β, γ (deg.)90.000, 90.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromosome partition protein Smc


Mass: 30232.598 Da / Num. of mol.: 1 / Fragment: UNP residues 345-468 and UNP residues 694-814
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus yayanosii (strain CH1 / JCM 16557) (archaea)
Strain: CH1 / JCM 16557 / Gene: smc, PYCH_01200 / Production host: Escherichia coli (E. coli) / References: UniProt: F8AFS8
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.18M HEPES (pH 7.0), 49% (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17619 / % possible obs: 94.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 28.62 Å2 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.025 / Net I/σ(I): 23.8
Reflection shellHighest resolution: 2 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 725 / % possible all: 78.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
HKLdata reduction
HKLdata scaling
RefinementResolution: 2→36.171 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 1768 10.03 %
Rwork0.2133 15851 -
obs0.218 17619 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.2 Å2 / Biso mean: 44.6777 Å2 / Biso min: 14.49 Å2
Refinement stepCycle: final / Resolution: 2→36.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 32 89 2018
Biso mean--58.07 43.48 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071931
X-RAY DIFFRACTIONf_angle_d0.9172579
X-RAY DIFFRACTIONf_chiral_restr0.041296
X-RAY DIFFRACTIONf_plane_restr0.004335
X-RAY DIFFRACTIONf_dihedral_angle_d25.3671243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9971-2.05110.34381060.2876962106875
2.0511-2.11150.281240.24541106123086
2.1115-2.17960.31191290.22491172130191
2.1796-2.25750.27581330.2291213134694
2.2575-2.34790.29331350.21881210134594
2.3479-2.45470.26851350.22061221135695
2.4547-2.58410.25241450.22021266141196
2.5841-2.74590.31571380.23131249138798
2.7459-2.95780.29611380.22361270140898
2.9578-3.25530.28891430.23021286142999
3.2553-3.7260.24571420.19991280142299
3.726-4.69270.22561500.17431281143199
4.6927-36.17710.221500.21771335148599

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