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- PDB-2p0j: Structure of restriction endonuclease BstYI bound to non-cognate DNA -

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Basic information

Entry
Database: PDB / ID: 2p0j
TitleStructure of restriction endonuclease BstYI bound to non-cognate DNA
Components
  • 5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3'
  • 5'-D(*TP*AP*TP*GP*GP*AP*TP*TP*CP*AP*T)-3'
  • BstYI
Keywordshydrolase/DNA / Restriction endonuclease / DNA recognition / scanning / hydrolase-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding / identical protein binding
Similarity search - Function
Type-2 restriction enzyme BglII / Restriction endonuclease BglII / Restriction endonuclease, type II, BamHI/BglIII/BstY / Restriction Endonuclease - #20 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / BstYI
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsTownson, S.A. / Samuelson, J.C. / Bao, Y. / Xu, S.Y. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2007
Title: BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning.
Authors: Townson, S.A. / Samuelson, J.C. / Bao, Y. / Xu, S.Y. / Aggarwal, A.K.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 21, 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

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3'
D: 5'-D(*TP*AP*TP*GP*GP*AP*TP*TP*CP*AP*T)-3'
A: BstYI
B: BstYI


Theoretical massNumber of molelcules
Total (without water)53,1504
Polymers53,1504
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.570, 118.990, 102.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-267-

HOH

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Components

#1: DNA chain 5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3'


Mass: 3341.224 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*AP*TP*GP*GP*AP*TP*TP*CP*AP*T)-3'


Mass: 3363.220 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein BstYI


Mass: 23222.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: bstYIR / Plasmid: PACYC, PCEF8, PET21AT / Production host: Escherichia coli (E. coli) / Strain (production host): ER2744 / References: UniProt: Q84AF2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M sodium citrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium citrate11
2HEPES11
3H2O11
4sodium citrate12
5HEPES12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.979, 0.968
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2003 / Details: mirrors
RadiationMonochromator: Si(III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9681
ReflectionResolution: 2.1→50 Å / Num. obs: 31206 / Redundancy: 7.7 %

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Phasing

PhasingMethod: MAD
Phasing dm shellResolution: 2.1→50 Å / Delta phi final: 0.123 / FOM : 0.126 / Reflection: 58103

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / FOM work R set: 0.835 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.239 5708 9.6 %
Rwork0.199 --
obs-58103 97.6 %
Solvent computationBsol: 59.379 Å2
Displacement parametersBiso mean: 27.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.868 Å20 Å20 Å2
2---0.554 Å20 Å2
3---1.421 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-2.1 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 445 0 334 3980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.218
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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