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- PDB-1b24: I-DMOI, INTRON-ENCODED ENDONUCLEASE -

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Basic information

Entry
Database: PDB / ID: 1b24
TitleI-DMOI, INTRON-ENCODED ENDONUCLEASE
ComponentsHoming endonuclease I-DmoI
KeywordsINTRON-ENCODED / ENDONUCLEASE / HOMING / THERMOSTABLE
Function / homology
Function and homology information


intein-mediated protein splicing / intron homing / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
LAGLIDADG-like domain / Intein / 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
Homing endonuclease I-DmoI
Similarity search - Component
Biological speciesDesulfurococcus mobilis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsVan Roey, P. / Silva, G.H.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI.
Authors: Silva, G.H. / Dalgaard, J.Z. / Belfort, M. / Van Roey, P.
History
DepositionDec 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homing endonuclease I-DmoI


Theoretical massNumber of molelcules
Total (without water)22,1811
Polymers22,1811
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.730, 37.220, 56.280
Angle α, β, γ (deg.)90.00, 112.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Homing endonuclease I-DmoI


Mass: 22181.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONYL PROTEIN / Source: (gene. exp.) Desulfurococcus mobilis (archaea) / Description: SELENOMETHIONINE AUXOTROPH / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3)
References: UniProt: P21505, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.01 Å3/Da / Density % sol: 33.3 % / Description: MAD DATA TREATED AS A SPECIAL CASE OF MIR
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP VAPOR-DIFFUSION METHOD: 4UL I-DMOI PROTEIN 1UL 20MM N-OCTYL-B- GLUCOPYRANOSIDE 4UL PRECIPITATING BUFFER: 30% PEG 3350 200MM SODIUM ACETATE 100MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
14UL I-DMOI PROTEIN11
21UL 20MM N-OCTYL-B-GLUCOPYRANOSIDE12
34UL PRECIPITATING BUFFER12
430% PEG 335012
5200MM SODIUM ACETATE12
6100MM TRIS-HCL PH 8.512
Crystal grow
*PLUS
Temperature: 310 K / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
25 mMTris-HCl1drop
3150 mM1dropNaCl
410 %ethylene glycol1drop
51 mMdithiothreitol1drop
62-3 %PEG33501reservoir
71-1.2 Msodium acetate1reservoir
810 %ethylene glycol1reservoir
950 mMsodium/potassium phosphate1reservoir
10100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9300,0.9785,0.9789
DetectorType: BRANDEIS / Detector: CCD / Date: Sep 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
20.97851
30.97891
ReflectionResolution: 2.2→20 Å / Num. obs: 8884 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rsym value: 0.059 / Net I/σ(I): 32.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6 % / Mean I/σ(I) obs: 24.7 / Rsym value: 0.07 / % possible all: 97.4
Reflection
*PLUS
Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.324 887 10 %RANDOM
Rwork0.218 ---
obs-8878 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 78 1505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.285
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.609
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3613 80 10 %
Rwork0.2996 737 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
X-RAY DIFFRACTION4PARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.609
LS refinement shell
*PLUS
Rfactor obs: 0.2996

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