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- PDB-5jdk: Crystal structure of the DNA binding domain of Sap1 in fission ye... -

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Basic information

Entry
Database: PDB / ID: 5jdk
TitleCrystal structure of the DNA binding domain of Sap1 in fission yeast S.pombe
ComponentsSwitch-activating protein 1
KeywordsDNA BINDING PROTEIN / DNA replication / alpha-helix
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 / SAD / Resolution: 0.998 Å
AuthorsHe, P. / Wang, T.
Funding support China, 2items
OrganizationGrant numberCountry
MOST2013CB911500 China
National Natural Science Foundation of China31300600 China
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe.
Authors: Guan, L. / He, P. / Yang, F. / Zhang, Y. / Hu, Y. / Ding, J. / Hua, Y. / Zhang, Y. / Ye, Q. / Hu, J. / Wang, T. / Jin, C. / Kong, D.
History
DepositionApr 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Switch-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2492
Polymers16,1571
Non-polymers921
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.840, 40.880, 70.140
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: 16156.630 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: sap1, SPCC1672.02c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40847
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.63 Å3/Da / Density % sol: 24.75 % / Description: hexagonal prism, Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 200mM Trimethylamine N-oxide, 15-22% (w/v) PEG 2000MME

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.97915
SEALED TUBERIGAKU21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 5, 2013
RIGAKU SATURN 944+2CCDSep 15, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
21.54181
Reflection

Entry-ID: 5JDK

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
0.998-17.875824099.91.26.60.04916.88
2.06-26.668919922241.57
Reflection shellResolution: 0.998→1.034 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.22 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-20000.98.691data reduction
CrystalClear1.44data scaling
PHENIX1.10.1phasing
RefinementMethod to determine structure: SAD / Resolution: 0.998→17.87 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.91
RfactorNum. reflection% reflection
Rfree0.1786 1997 3.43 %
Rwork0.1696 --
obs0.1699 58139 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.998→17.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 6 200 1077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006897
X-RAY DIFFRACTIONf_angle_d0.9111203
X-RAY DIFFRACTIONf_dihedral_angle_d16.824360
X-RAY DIFFRACTIONf_chiral_restr0.068131
X-RAY DIFFRACTIONf_plane_restr0.006154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.998-1.0230.28811380.29673884X-RAY DIFFRACTION98
1.023-1.05060.28491400.26673941X-RAY DIFFRACTION100
1.0506-1.08150.26631410.24723973X-RAY DIFFRACTION100
1.0815-1.11640.22421400.21223977X-RAY DIFFRACTION100
1.1164-1.15630.19381410.18643948X-RAY DIFFRACTION100
1.1563-1.20260.19081420.18023995X-RAY DIFFRACTION100
1.2026-1.25730.20711420.18433970X-RAY DIFFRACTION100
1.2573-1.32360.2111430.17463998X-RAY DIFFRACTION100
1.3236-1.40650.17991420.16754007X-RAY DIFFRACTION100
1.4065-1.51510.18031420.15834002X-RAY DIFFRACTION100
1.5151-1.66740.16941440.15014027X-RAY DIFFRACTION100
1.6674-1.90850.16831450.16014056X-RAY DIFFRACTION100
1.9085-2.40370.15251460.15384113X-RAY DIFFRACTION100
2.4037-18.42310.1611510.15824251X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.3255 Å / Origin y: 1.9302 Å / Origin z: 79.2675 Å
111213212223313233
T0.0473 Å20.0005 Å20.002 Å2-0.0473 Å2-0.0004 Å2--0.0437 Å2
L0.2468 °20.1037 °20.1617 °2-0.5216 °2-0.0014 °2--0.4605 °2
S0.0069 Å °0.0253 Å °0.0536 Å °-0.0109 Å °-0.0135 Å °0.0173 Å °0.0052 Å °-0.0067 Å °0.0074 Å °
Refinement TLS groupSelection details: chain 'A'

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