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- PDB-1w1w: Sc Smc1hd:Scc1-C complex, ATPgS -

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Basic information

Entry
Database: PDB / ID: 1w1w
TitleSc Smc1hd:Scc1-C complex, ATPgS
Components
  • SISTER CHROMATID COHESION PROTEIN 1
  • STRUCTURAL MAINTENANCE OF CHROMOSOME 1
KeywordsCELL ADHESION / COHESIN / CHROMOSOME SEGREGATION / KLEISIN / MITOSIS / CELL CYCLE
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / DNA secondary structure binding / cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / DNA secondary structure binding / cohesin complex / SUMOylation of DNA damage response and repair proteins / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / sister chromatid cohesion / mitotic sister chromatid cohesion / protein acetylation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / chromosome, centromeric region / condensed nuclear chromosome / double-strand break repair / double-stranded DNA binding / cell division / apoptotic process / DNA damage response / chromatin binding / protein kinase binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Structural maintenance of chromosome 1. Chain E / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge ...Structural maintenance of chromosome 1. Chain E / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / 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 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Structural maintenance of chromosomes protein 1 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsHaering, C. / Nasmyth, K. / Lowe, J.
CitationJournal: Mol. Cell / Year: 2004
Title: Structure and stability of cohesin's Smc1-kleisin interaction.
Authors: Haering, C.H. / Schoffnegger, D. / Nishino, T. / Helmhart, W. / Nasmyth, K. / Lowe, J.
History
DepositionJun 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
B: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
C: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
D: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
E: SISTER CHROMATID COHESION PROTEIN 1
F: SISTER CHROMATID COHESION PROTEIN 1
G: SISTER CHROMATID COHESION PROTEIN 1
H: SISTER CHROMATID COHESION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,24616
Polymers250,0568
Non-polymers2,1908
Water0
1
B: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
F: SISTER CHROMATID COHESION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0614
Polymers62,5142
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-28 kcal/mol
Surface area18720 Å2
MethodPISA
2
A: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
E: SISTER CHROMATID COHESION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0614
Polymers62,5142
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-28 kcal/mol
Surface area16220 Å2
MethodPISA
3
D: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
H: SISTER CHROMATID COHESION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0614
Polymers62,5142
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-27.9 kcal/mol
Surface area18650 Å2
MethodPISA
4
C: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
G: SISTER CHROMATID COHESION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0614
Polymers62,5142
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-27.6 kcal/mol
Surface area18760 Å2
MethodPISA
5
A: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
B: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
E: SISTER CHROMATID COHESION PROTEIN 1
F: SISTER CHROMATID COHESION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1238
Polymers125,0284
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
C: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
D: STRUCTURAL MAINTENANCE OF CHROMOSOME 1
G: SISTER CHROMATID COHESION PROTEIN 1
H: SISTER CHROMATID COHESION PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1238
Polymers125,0284
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.465, 138.465, 284.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
STRUCTURAL MAINTENANCE OF CHROMOSOME 1 / SMC1 / DA-BOX PROTEIN SMC1


Mass: 48789.484 Da / Num. of mol.: 4 / Fragment: HEAD DOMAIN RESIDUES 1-214,1024-1225
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-214, ESSKHPTSLVPRGS LINKER, 1024-1225
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32908
#2: Protein
SISTER CHROMATID COHESION PROTEIN 1 / SCC1


Mass: 13724.415 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN RESIDUES 451-563
Source method: isolated from a genetically manipulated source
Details: RESIDUES 451-566
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12158
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 64 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→57 Å / Num. obs: 59522 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.2 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 3065 4.9 %RANDOM
Rwork0.2417 ---
obs0.2417 61245 98.8 %-
Solvent computationBsol: 29.9012 Å2 / ksol: 0.314107 e/Å3
Displacement parametersBiso mean: 66.24 Å2
Baniso -1Baniso -2Baniso -3
1-5.328 Å20 Å20 Å2
2--5.328 Å20 Å2
3----10.656 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12232 0 128 0 12360
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.456
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→2.92 Å / Rfactor Rfree: 0.3937 / Rfactor Rwork: 0.3969 / Total num. of bins used: 50
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4AGS.PARAM

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