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- PDB-6exu: Crystal structure of the DNA binding domain of fission yeast Sap1 -

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Basic information

Entry
Database: PDB / ID: 6exu
TitleCrystal structure of the DNA binding domain of fission yeast Sap1
ComponentsSwitch-activating protein 1
KeywordsDNA BINDING PROTEIN / S. pombe / mating type switch / DNA replication / myb domain
Function / homology
Function and homology information


site-specific DNA replication termination / mitotic pre-replicative complex assembly / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / gene conversion at mating-type locus / DNA binding, bending / chromosome segregation / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromatin ...site-specific DNA replication termination / mitotic pre-replicative complex assembly / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / gene conversion at mating-type locus / DNA binding, bending / chromosome segregation / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromatin / DNA binding / nucleus
Similarity search - Function
: / Switch activating protein 1, N-terminal
Similarity search - Domain/homology
Switch-activating protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.409 Å
AuthorsEkundayo, B. / Joergensen, M. / Schalch, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation SNFPP00P3_139137, PP00P3_163760_1, PP00P3_172904 Switzerland
CitationJournal: Sci Rep / Year: 2018
Title: Structure of the replication regulator Sap1 reveals functionally important interfaces.
Authors: Jorgensen, M.M. / Ekundayo, B. / Zaratiegui, M. / Skriver, K. / Thon, G. / Schalch, T.
History
DepositionNov 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Switch-activating protein 1


Theoretical massNumber of molelcules
Total (without water)13,9361
Polymers13,9361
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.582, 40.831, 70.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Switch-activating protein 1


Mass: 13936.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: sap1, SPCC1672.02c / Production host: Escherichia coli (E. coli) / References: UniProt: P40847
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.85 Å3/Da / Density % sol: 33.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M SPG buffer (Succinic Acid, Phosphate, Glycine) pH 7.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 21, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→35.39 Å / Num. obs: 20477 / % possible obs: 99.49 % / Redundancy: 2 % / Rmerge(I) obs: 0.02145 / Net I/σ(I): 24.76
Reflection shellResolution: 1.409→1.459 Å / Rmerge(I) obs: 0.1886 / Mean I/σ(I) obs: 4.62 / Num. unique all: 1969 / % possible all: 96.52

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementResolution: 1.409→35.39 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.29
RfactorNum. reflection% reflection
Rfree0.1982 1028 5.02 %
Rwork0.1689 --
obs0.1703 20477 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.409→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 0 125 1002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008895
X-RAY DIFFRACTIONf_angle_d0.9731201
X-RAY DIFFRACTIONf_dihedral_angle_d19.63356
X-RAY DIFFRACTIONf_chiral_restr0.063129
X-RAY DIFFRACTIONf_plane_restr0.006155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.409-1.48330.25771420.22042654X-RAY DIFFRACTION97
1.4833-1.57620.19711610.18452720X-RAY DIFFRACTION100
1.5762-1.69790.2281410.17272765X-RAY DIFFRACTION100
1.6979-1.86880.20951580.17482751X-RAY DIFFRACTION100
1.8688-2.13910.21541400.16592775X-RAY DIFFRACTION100
2.1391-2.6950.18271290.15892833X-RAY DIFFRACTION100
2.695-35.40120.18251570.16462951X-RAY DIFFRACTION100

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