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- PDB-3r3p: Homing Endonuclease I-Bth0305I Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 3r3p
TitleHoming Endonuclease I-Bth0305I Catalytic Domain
ComponentsMobile intron protein
KeywordsHYDROLASE / homing endonuclease
Function / homologyDomain of unknown function DUF559 / Protein of unknown function (DUF559) / Endonuclease; Chain A / VSR Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta / Mobile intron protein
Function and homology information
Biological speciesBacillus phage 0305phi8-36 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTaylor, G.K. / Stoddard, B.L.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family.
Authors: Taylor, G.K. / Heiter, D.F. / Pietrokovski, S. / Stoddard, B.L.
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mobile intron protein
B: Mobile intron protein


Theoretical massNumber of molelcules
Total (without water)24,4722
Polymers24,4722
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-3 kcal/mol
Surface area10860 Å2
MethodPISA
2
A: Mobile intron protein
B: Mobile intron protein

A: Mobile intron protein
B: Mobile intron protein


Theoretical massNumber of molelcules
Total (without water)48,9444
Polymers48,9444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6700 Å2
ΔGint-20 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.292, 52.292, 133.787
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 Mobile intron protein


Mass: 12235.967 Da / Num. of mol.: 2 / Fragment: UNP Residues 167-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage 0305phi8-36 (virus) / Gene: ORF029, 0305phi8-36p029 / Production host: Escherichia coli (E. coli) / References: UniProt: A7KV39
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.87 Å3/Da / Density % sol: 34.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 50 mM Tris, 100 mM LiSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2010
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 9728 / Num. obs: 9728 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.24198.3
2.24-2.281100
2.28-2.321100
2.32-2.371100

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.198 Å / SU ML: 0.3 / σ(F): 0.22 / Phase error: 24.3 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2612 973 10 %
Rwork0.2158 --
obs0.2204 9727 96.82 %
all-10700 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.297 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0755 Å20 Å2-0 Å2
2--3.0755 Å20 Å2
3----6.151 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 0 29 1655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021660
X-RAY DIFFRACTIONf_angle_d0.4862238
X-RAY DIFFRACTIONf_dihedral_angle_d10.069618
X-RAY DIFFRACTIONf_chiral_restr0.037246
X-RAY DIFFRACTIONf_plane_restr0.001278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.31640.3181230.25341108X-RAY DIFFRACTION88
2.3164-2.46150.30131360.23711220X-RAY DIFFRACTION97
2.4615-2.65150.28971360.23291222X-RAY DIFFRACTION97
2.6515-2.91830.28151370.2241241X-RAY DIFFRACTION97
2.9183-3.34040.27581410.23381260X-RAY DIFFRACTION99
3.3404-4.20790.27211430.1951298X-RAY DIFFRACTION99
4.2079-41.20520.21411570.2051405X-RAY DIFFRACTION100

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