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- PDB-2cw7: Crystal structure of intein homing endonuclease II -

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Basic information

Entry
Database: PDB / ID: 2cw7
TitleCrystal structure of intein homing endonuclease II
ComponentsEndonuclease PI-PkoII
KeywordsHYDROLASE
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / exonuclease activity / DNA-templated DNA replication / endonuclease activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
Intein homing endonuclease, domain IV / Intein homing endonuclease, domain III / DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / Intein splicing domain / Intein / Homing endonucleases ...Intein homing endonuclease, domain IV / Intein homing endonuclease, domain III / DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / Intein splicing domain / Intein / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Helicase, Ruva Protein; domain 3 / Beta Complex / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMatsumura, H. / Takahashi, H. / Inoue, T. / Hashimoto, H. / Nishioka, M. / Fujiwara, S. / Takagi, M. / Imanaka, T. / Kai, Y.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1
Authors: Matsumura, H. / Takahashi, H. / Inoue, T. / Yamamoto, T. / Hashimoto, H. / Nishioka, M. / Fujiwara, S. / Takagi, M. / Imanaka, T. / Kai, Y.
History
DepositionJun 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease PI-PkoII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5734
Polymers62,2851
Non-polymers2883
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.700, 149.060, 146.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Endonuclease PI-PkoII


Mass: 62284.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pET8C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P77933, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.58 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, Sodium phosphate, Sodium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 30434 / Num. obs: 30434 / % possible obs: 93.2 % / Observed criterion σ(I): 1.7 / Redundancy: 3.9 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 1.7 / % possible all: 79.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMET PI-TkoII

Resolution: 2.7→38.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 315160.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1512 5 %RANDOM
Rwork0.206 ---
obs0.206 30416 93.2 %-
all-30427 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.3582 Å2 / ksol: 0.309601 e/Å3
Displacement parametersBiso mean: 58.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.08 Å20 Å20 Å2
2--1.94 Å20 Å2
3----7.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.91 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 15 19 4426
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 232 5.3 %
Rwork0.358 4110 -
obs--80.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gll.paramgll.top

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