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- PDB-1dq3: CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEA... -

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Basic information

Entry
Database: PDB / ID: 1dq3
TitleCRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI
ComponentsENDONUCLEASE
KeywordsHYDROLASE / Endonuclease / PI-PfuI / Intein-encoded
Function / homology
Function and homology information


cobalamin binding / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / intein-mediated protein splicing / endonuclease activity / DNA replication / Hydrolases; Acting on ester bonds / ATP binding
Similarity search - Function
Double Stranded RNA Binding Domain - #90 / Ribonucleotide reductase, stirrup / PI-PfuI intein endonuclease, subdomain / Stirrup / PI-PfuI Endonuclease subdomain / Ribonucleotide reductase, adenosylcobalamin-dependent / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / ATP-cone domain / ATP cone domain ...Double Stranded RNA Binding Domain - #90 / Ribonucleotide reductase, stirrup / PI-PfuI intein endonuclease, subdomain / Stirrup / PI-PfuI Endonuclease subdomain / Ribonucleotide reductase, adenosylcobalamin-dependent / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / LAGLIDADG-like domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel 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 / Double Stranded RNA Binding Domain / Beta Complex / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Vitamin B12-dependent ribonucleoside-diphosphate reductase / Vitamin B12-dependent ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsIchiyanagi, K. / Ishino, Y. / Morikawa, K.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.
Authors: Ichiyanagi, K. / Ishino, Y. / Ariyoshi, M. / Komori, K. / Morikawa, K.
History
DepositionDec 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2262
Polymers53,1601
Non-polymers651
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.550, 85.280, 65.410
Angle α, β, γ (deg.)90.00, 112.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDONUCLEASE /


Mass: 53160.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P95484, UniProt: E7FHX6*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 6.5
Details: PEG4000, bis tris, sodium chloride, dioxane, glycerol, pH 6.5, MICRODIALYSIS, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
250 mMBis-Tris-HCl11
30.5 M11NaCl
45 %(w/v)PEG400011
510 %(v/v)dioxane11
610 %glycerol11
72 mM2-mercaptoethanol11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: May 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 31152 / % possible obs: 93.1 % / Redundancy: 2 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.255 / % possible all: 84.9
Reflection
*PLUS
% possible obs: 93.7 %
Reflection shell
*PLUS
% possible obs: 84.9 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→30 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1579 5.1 %RANDOM
Rwork0.192 ---
obs0.192 31152 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.9175 Å2 / ksol: 0.335606 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å20 Å2-0.15 Å2
2--6.97 Å20 Å2
3----3.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3755 0 1 332 4088
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it2.691.5
X-RAY DIFFRACTIONc_mcangle_it3.922
X-RAY DIFFRACTIONc_scbond_it4.152
X-RAY DIFFRACTIONc_scangle_it6.042.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.314 183 5.4 %
Rwork0.28 3223 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / Rfactor Rwork: 0.281

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