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- PDB-5nnv: Structure of a Bacillus subtilis Smc coiled coil middle fragment -

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Basic information

Entry
Database: PDB / ID: 5nnv
TitleStructure of a Bacillus subtilis Smc coiled coil middle fragment
ComponentsChromosome partition protein Smc,Chromosome partition protein Smc
KeywordsCELL CYCLE / Smc Chromosome Segregation / DNA binding protein
Function / homology
Function and homology information


chromosome condensation / sister chromatid cohesion / chromosome segregation / chromosome / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / identical protein 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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.295 Å
AuthorsDiebold-Durand, M.-L. / Basquin, J. / Gruber, S.
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 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosome partition protein Smc,Chromosome partition protein Smc
B: Chromosome partition protein Smc,Chromosome partition protein Smc
C: Chromosome partition protein Smc,Chromosome partition protein Smc
D: Chromosome partition protein Smc,Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)129,3074
Polymers129,3074
Non-polymers00
Water00
1
A: Chromosome partition protein Smc,Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)32,3271
Polymers32,3271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chromosome partition protein Smc,Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)32,3271
Polymers32,3271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chromosome partition protein Smc,Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)32,3271
Polymers32,3271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chromosome partition protein Smc,Chromosome partition protein Smc


Theoretical massNumber of molelcules
Total (without water)32,3271
Polymers32,3271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.309, 42.739, 174.601
Angle α, β, γ (deg.)89.97, 93.64, 89.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Chromosome partition protein Smc,Chromosome partition protein Smc


Mass: 32326.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: smc, ylqA, BSU15940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51834
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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 11% PEG3350 50mM Tris pH8 4% MPD 200mM Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.295→87.125 Å / Num. obs: 37323 / % possible obs: 98.54 % / Redundancy: 3.6 % / Net I/σ(I): 12.33
Reflection shellResolution: 3.295→3.48 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.8 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.295→50 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2983 1780 4.77 %
Rwork0.262 --
obs0.2632 37323 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.295→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 0 0 6042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036050
X-RAY DIFFRACTIONf_angle_d0.8568267
X-RAY DIFFRACTIONf_dihedral_angle_d13.5651874
X-RAY DIFFRACTIONf_chiral_restr0.0291081
X-RAY DIFFRACTIONf_plane_restr0.0031123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2979-3.39330.35221640.29962922X-RAY DIFFRACTION91
3.3933-3.50080.34321800.2962796X-RAY DIFFRACTION91
3.5008-3.62340.29142250.2912878X-RAY DIFFRACTION90
3.6234-3.76510.31151540.27262913X-RAY DIFFRACTION92
3.7651-3.9320.2981690.26472844X-RAY DIFFRACTION91
3.932-4.1330.3081040.26462970X-RAY DIFFRACTION94
4.133-4.38270.2809750.25952995X-RAY DIFFRACTION94
4.3827-4.70640.2453870.22623002X-RAY DIFFRACTION95
4.7064-5.15330.2828960.26482922X-RAY DIFFRACTION94
5.1533-5.83970.34752500.30132788X-RAY DIFFRACTION90
5.8397-7.15020.30891300.29772997X-RAY DIFFRACTION93
7.1502-13.05140.2345990.21112935X-RAY DIFFRACTION93

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