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- PDB-4rsi: Yeast Smc2-Smc4 hinge domain with extended coiled coils -

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Basic information

Entry
Database: PDB / ID: 4rsi
TitleYeast Smc2-Smc4 hinge domain with extended coiled coils
Components
  • Structural maintenance of chromosomes protein 2
  • Structural maintenance of chromosomes protein 4
KeywordsCELL CYCLE / Smc hinge domain with coiled coil / chromosomal condensation
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / condensin complex / DNA secondary structure binding / rDNA chromatin condensation / mitotic chromosome condensation / chromosome condensation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / condensin complex / DNA secondary structure binding / rDNA chromatin condensation / mitotic chromosome condensation / chromosome condensation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / condensed chromosome / double-stranded DNA binding / cell division / chromatin binding / chromatin / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Smc2, ATP-binding cassette domain / 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
PHOSPHATE ION / Structural maintenance of chromosomes protein 2 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsSoh, Y.M. / Shin, H.C. / Oh, B.H.
CitationJournal: Mol.Cell / Year: 2015
Title: Molecular Basis for SMC Rod Formation and Its Dissolution upon DNA Binding.
Authors: Soh, Y.M. / Burmann, F. / Shin, H.C. / Oda, T. / Jin, K.S. / Toseland, C.P. / Kim, C. / Lee, H. / Kim, S.J. / Kong, M.S. / Durand-Diebold, M.L. / Kim, Y.G. / Kim, H.M. / Lee, N.K. / Sato, M. ...Authors: Soh, Y.M. / Burmann, F. / Shin, H.C. / Oda, T. / Jin, K.S. / Toseland, C.P. / Kim, C. / Lee, H. / Kim, S.J. / Kong, M.S. / Durand-Diebold, M.L. / Kim, Y.G. / Kim, H.M. / Lee, N.K. / Sato, M. / Oh, B.H. / Gruber, S.
History
DepositionNov 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 2
B: Structural maintenance of chromosomes protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8044
Polymers90,6142
Non-polymers1902
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-20 kcal/mol
Surface area38580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.259, 49.707, 154.283
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Structural maintenance of chromosomes protein 2 / DA-box protein SMC2


Mass: 45382.734 Da / Num. of mol.: 1 / Fragment: Smc2 hinge
Source method: isolated from a genetically manipulated source
Details: separate expression co-purification
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: Saccharomyces cerevisiae, SMC2, YFR031C / Plasmid: pProExHTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: P38989
#2: Protein Structural maintenance of chromosomes protein 4


Mass: 45231.340 Da / Num. of mol.: 1 / Fragment: Smc4 hinge
Source method: isolated from a genetically manipulated source
Details: stop codon, culture in minimal media, co-purification
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: L9449.5, Saccharomyces cerevisiae, SMC4, YLR086W / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) RIL / References: UniProt: Q12267
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG 300, 0.1 M Na/K phosphate pH 6.0, 8% glycerol, 10 mM dithiothreitol (DTT), VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: Numerical link type double crystal monochromator, liquid nitrogen cooling Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 49139 / Num. obs: 28485 / % possible obs: 90.2 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 4.4 % / Rsym value: 0.09 / Net I/σ(I): 33.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→38.922 Å / SU ML: 0.44 / σ(F): 1.85 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 2776 5.65 %5% random
Rwork0.2227 ---
all-49139 --
obs-28485 80.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→38.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5234 0 10 8 5252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015308
X-RAY DIFFRACTIONf_angle_d1.2877158
X-RAY DIFFRACTIONf_dihedral_angle_d17.7032021
X-RAY DIFFRACTIONf_chiral_restr0.077831
X-RAY DIFFRACTIONf_plane_restr0.006929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.950.3826800.33861606X-RAY DIFFRACTION56
2.95-3.00360.34371050.34041607X-RAY DIFFRACTION57
3.0036-3.06140.3971980.35061722X-RAY DIFFRACTION60
3.0614-3.12380.34981180.33031876X-RAY DIFFRACTION64
3.1238-3.19170.36741160.29411957X-RAY DIFFRACTION69
3.1917-3.2660.3151180.29682054X-RAY DIFFRACTION73
3.266-3.34760.32951210.26462251X-RAY DIFFRACTION77
3.3476-3.4380.3341440.24322340X-RAY DIFFRACTION82
3.438-3.53910.25561540.23472442X-RAY DIFFRACTION84
3.5391-3.65330.30581510.2332450X-RAY DIFFRACTION87
3.6533-3.78380.2681460.23192588X-RAY DIFFRACTION89
3.7838-3.93510.24031650.21172490X-RAY DIFFRACTION88
3.9351-4.1140.27361530.20442643X-RAY DIFFRACTION90
4.114-4.33070.26111460.20082583X-RAY DIFFRACTION92
4.3307-4.60160.23061670.18092693X-RAY DIFFRACTION93
4.6016-4.95620.23871650.17662726X-RAY DIFFRACTION93
4.9562-5.45380.26351710.18712648X-RAY DIFFRACTION94
5.4538-6.24020.27481550.21622714X-RAY DIFFRACTION94
6.2402-7.85140.20171690.20342695X-RAY DIFFRACTION95
7.8514-38.92580.23671340.21642278X-RAY DIFFRACTION79

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