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- PDB-5xei: Crystal structure of the Smc head domain with a coiled coil and j... -

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Basic information

Entry
Database: PDB / ID: 5xei
TitleCrystal structure of the Smc head domain with a coiled coil and joint derived from Pyrococcus yayanosii
ComponentsChromosome partition protein Smc
KeywordsDNA BINDING PROTEIN / CELL CYCLE / Condensin / Smc / head domain / ABC-ATPase
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome segregation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsLee, H. / Noh, 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 5, 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 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)60,8251
Polymers60,8251
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27620 Å2
Unit cell
Length a, b, c (Å)120.320, 50.836, 122.057
Angle α, β, γ (deg.)90.000, 118.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromosome partition protein Smc


Mass: 60825.113 Da / Num. of mol.: 1 / Fragment: UNP residues 1-254 and 907-1177
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 7% PEG 3350, 4% Tacsimate pH4.0

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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 S 6M / Detector: PIXEL / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.599→50 Å / Num. obs: 18871 / % possible obs: 92.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 50.93 Å2 / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNS

5xns


Resolution: 2.599→39.625 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 1903 10.08 %
Rwork0.2075 16968 -
obs0.2145 18871 92.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.22 Å2 / Biso mean: 64.9606 Å2 / Biso min: 29.48 Å2
Refinement stepCycle: final / Resolution: 2.599→39.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 0 13 4100
Biso mean---49.81 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014136
X-RAY DIFFRACTIONf_angle_d1.1815539
X-RAY DIFFRACTIONf_chiral_restr0.056622
X-RAY DIFFRACTIONf_plane_restr0.007719
X-RAY DIFFRACTIONf_dihedral_angle_d21.1652611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5994-2.66440.3532930.313888898170
2.6644-2.73640.40341220.30131053117581
2.7364-2.81690.3391310.30271165129689
2.8169-2.90780.32631320.28731141127389
2.9078-3.01170.33421280.26171166129490
3.0117-3.13220.31931360.24941183131991
3.1322-3.27470.30621390.23221234137395
3.2747-3.44730.30281370.21471278141598
3.4473-3.66310.27151460.20611283142998
3.6631-3.94570.28651440.19781284142899
3.9457-4.34230.29571510.18771305145699
4.3423-4.96960.21391440.159413051449100
4.9696-6.25720.2731460.19681323146999
6.2572-39.62960.22761540.17941360151499

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