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- PDB-6x1j: The homing endonuclease I-WcaI bound to its DNA recognition sequence -

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Basic information

Entry
Database: PDB / ID: 6x1j
TitleThe homing endonuclease I-WcaI bound to its DNA recognition sequence
Components
  • (DNA (25-mer)) x 2
  • Probable intron-encoded endonuclease 1
KeywordsHYDROLASE / intron-encoded DNA homing endonuclease / enzyme / protein-DNA interactions / isoschizomers
Function / homology
Function and homology information


Group II intron splicing / intron homing / mRNA cis splicing, via spliceosome / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
: / LAGLIDADG DNA endonuclease family / Homing endonuclease, LAGLIDADG / Homing endonuclease
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Probable intron-encoded endonuclease 1
Similarity search - Component
Biological speciesWickerhamomyces canadensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.945 Å
AuthorsNawimanage, R. / Lohman, J.R. / Gimble, F.S.
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structure-Function Studies of Two Yeast Homing Endonucleases that Evolved to Cleave Identical Targets with Dissimilar Rates and Specificities.
Authors: Nawimanage, R.R. / Yuan, Z. / Casares, M. / Joshi, R. / Lohman, J.R. / Gimble, F.S.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable intron-encoded endonuclease 1
C: DNA (25-mer)
D: DNA (25-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3697
Polymers43,2133
Non-polymers1564
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-53 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.601, 37.281, 94.064
Angle α, β, γ (deg.)90.000, 100.440, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

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Components

#1: Protein Probable intron-encoded endonuclease 1


Mass: 27855.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wickerhamomyces canadensis (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q34807, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (25-mer)


Mass: 7741.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Wickerhamomyces canadensis (fungus)
#3: DNA chain DNA (25-mer)


Mass: 7615.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Wickerhamomyces canadensis (fungus)
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.09 % / Description: Needles
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21% PEG 3350, 0.1M Tris-HCl, 0.2M Lithium sulfate, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 17, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.945→30 Å / Num. obs: 33735 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.964 / CC star: 0.991 / Rpim(I) all: 0.104 / Rrim(I) all: 0.198 / Χ2: 1.063 / Net I/σ(I): 6.5
Reflection shellResolution: 1.945→2.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3306 / CC1/2: 0.807 / CC star: 0.945 / Rpim(I) all: 0.461 / Rrim(I) all: 0.858 / Χ2: 0.882 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.42 Å29.86 Å
Translation6.42 Å29.86 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.6.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R7M

1r7m


Resolution: 1.945→29.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.699 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1627 4.8 %RANDOM
Rwork0.2272 ---
obs0.229 31986 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.33 Å2 / Biso mean: 37.752 Å2 / Biso min: 12.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0.01 Å2
2---0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.945→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 1004 4 141 3075
Biso mean--38.92 35.54 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123202
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182483
X-RAY DIFFRACTIONr_angle_refined_deg1.761.4584468
X-RAY DIFFRACTIONr_angle_other_deg1.4071.9125818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0735.498483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75924.257101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93515398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.072155
X-RAY DIFFRACTIONr_chiral_restr0.1360.23446
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02656
LS refinement shellResolution: 1.9451→1.996 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.44 96 -
Rwork0.421 1650 -
obs--69.9 %

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