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- PDB-1sdo: Crystal Structure of Restriction Endonuclease BstYI -

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Basic information

Entry
Database: PDB / ID: 1sdo
TitleCrystal Structure of Restriction Endonuclease BstYI
ComponentsBstYI
KeywordsHYDROLASE / Restriction Endonuclease
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/BglIII / 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
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsTownson, S.A. / Samuelson, J.C. / Vanamee, E.S. / Edwards, T.A. / Escalante, C.R. / Xu, S.Y. / Aggarwal, A.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of BstYI at 1.85 A Resolution: A Thermophilic Restriction Endonuclease with Overlapping Specificities to BamHI and BglII
Authors: Townson, S.A. / Samuelson, J.C. / Vanamee, E.S. / Edwards, T.A. / Escalante, C.R. / Xu, S.Y. / Aggarwal, A.K.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: BstYI


Theoretical massNumber of molelcules
Total (without water)23,2231
Polymers23,2231
Non-polymers00
Water1,62190
1
A: BstYI

A: BstYI


Theoretical massNumber of molelcules
Total (without water)46,4452
Polymers46,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)69.890, 76.610, 78.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThis entry contains the crystallographic asymmetric unit which consists of a monomer (1 chain). The biological dimer is generated by the operations: Rotation Matrix -1.00000 0.00002 0.00000 0.00002 1.00000 -0.00004 0.00000 -0.00004 -1.00000 Translation 69.89 0.0094 78.9707

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Components

#1: Protein BstYI


Mass: 23222.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: BSTYIR / Production host: Escherichia coli (E. coli) / Strain (production host): ER2744
References: UniProt: Q84AF2, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG-400, 0.1M HEPES, 200mM Calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.973, 0.9282
DetectorType: SBC-2 / Detector: CCD / Date: Jan 1, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9731
20.92821
ReflectionResolution: 1.85→50 Å / Num. all: 34966 / Num. obs: 33604 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.092 / Rsym value: 0.085 / Net I/σ(I): 17.4

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Processing

Software
NameClassification
DENZOdata reduction
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3273 -RANDOM
Rwork0.22 ---
all-34966 --
obs-33604 96.1 %-
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.915 Å20 Å20 Å2
2---7.148 Å20 Å2
3---5.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-1.85 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 0 90 1637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.00709
X-RAY DIFFRACTIONc_angle_deg1.2909
X-RAY DIFFRACTIONc_dihedral_angle_d21.93
X-RAY DIFFRACTIONc_improper_angle_d0.829

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