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- PDB-2dch: Crystal structure of archaeal intron-encoded homing endonuclease ... -

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Basic information

Entry
Database: PDB / ID: 2dch
TitleCrystal structure of archaeal intron-encoded homing endonuclease I-Tsp061I
Componentsputative homing endonuclease
KeywordsHYDROLASE / alpha/beta fold
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
LAGLIDADG-like domain / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Putative homing endonuclease
Similarity search - Component
Biological speciesThermoproteus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.06 Å
AuthorsNakayama, H. / Tsuge, H. / Shimamura, T. / Miyano, M. / Nomura, N. / Sako, Y.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of a hyperthermophilic archaeal homing endonuclease, I-Tsp061I: contribution of cross-domain polar networks to thermostability.
Authors: Nakayama, H. / Shimamura, T. / Imagawa, T. / Shirai, N. / Itoh, T. / Sako, Y. / Miyano, M. / Sakuraba, H. / Ohshima, T. / Nomura, N. / Tsuge, H.
History
DepositionJan 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Database references
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: putative homing endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8904
Polymers24,6621
Non-polymers2283
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: putative homing endonuclease
hetero molecules

X: putative homing endonuclease
hetero molecules

X: putative homing endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,67012
Polymers73,9873
Non-polymers6839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7720 Å2
ΔGint-150 kcal/mol
Surface area26270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.593, 91.593, 193.643
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assemly is a monomer generated by the two domains connected by the linker loop.

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Components

#1: Protein putative homing endonuclease / Archaeal intron-encoded DNA endonuclease


Mass: 24662.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus (archaea) / Genus: Thermoproteus / Strain: IC-061 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q8J309, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS BELIEVE THAT LEU 26 AND VAL 63 ARE CORRECT AND THAT DATABASE IS INCORRECT AT THESE POSITIONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 2.2M ammonium sulfate, 0.05M sodium citrate, pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeID
SYNCHROTRONPhoton Factory BL-6A1
ROTATING ANODERIGAKU2
Detector
TypeIDDetectorDate
RIGAKU RAXIS VII1IMAGE PLATEMay 13, 2003
2CCDJun 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.06→72.55 Å / Num. obs: 19290 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.062 / Net I/σ(I): 36.9
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1965 / Rsym value: 0.259 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.06→72.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.025 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24259 986 5.1 %RANDOM
Rwork0.20165 ---
obs0.20372 18302 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.012 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.06→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 11 172 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9642284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46922.89576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40915301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3451514
X-RAY DIFFRACTIONr_chiral_restr0.1060.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021262
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2771
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4441.51037
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98321626
X-RAY DIFFRACTIONr_scbond_it2.9753751
X-RAY DIFFRACTIONr_scangle_it4.1754.5658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.057→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 77 -
Rwork0.242 1288 -
obs--95.25 %

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