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Basic information

Entry
Database: PDB / ID: 1mow
TitleE-DreI
Components
  • 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
  • chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI
KeywordsHydrolase/DNA / LAGLIDADG / homing / engineering / design / endonuclease / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / identical protein binding
Similarity search - Function
LAGLIDADG endonuclease / 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
DNA / DNA (> 10) / DNA endonuclease I-CreI / Homing endonuclease I-DmoI
Similarity search - Component
Biological speciesDesulfurococcus mobilis (archaea)
Chlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChevalier, B.S. / Kortemme, T. / Chadsey, M.S. / Baker, D. / Monnat Jr., R.J. / Stoddard, B.L.
CitationJournal: Mol.Cell / Year: 2002
Title: Design, Activity and Structure of a Highly Specific Artificial Endonuclease
Authors: Chevalier, B.S. / Kortemme, T. / Chadsey, M.S. / Baker, D. / Monnat Jr., R.J. / Stoddard, B.L.
History
DepositionSep 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
C: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
E: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
F: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
H: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
I: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
K: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
L: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
A: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI
D: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI
G: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI
J: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,35946
Polymers176,59512
Non-polymers2,76434
Water8,179454
1
B: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
C: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
A: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,62721
Polymers44,1493
Non-polymers1,47818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
F: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
D: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,43519
Polymers44,1493
Non-polymers1,28616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
I: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
G: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI


Theoretical massNumber of molelcules
Total (without water)44,1493
Polymers44,1493
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
K: 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'
L: 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'
J: chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI


Theoretical massNumber of molelcules
Total (without water)44,1493
Polymers44,1493
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.760, 131.760, 120.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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DNA chain , 2 types, 8 molecules BEHKCFIL

#1: DNA chain
5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP*CP*GP*GP*CP*G)-3'


Mass: 7001.524 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA target site (top strand)
#2: DNA chain
5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3'


Mass: 7121.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA target site (bottom strand)

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Protein , 1 types, 4 molecules ADGJ

#3: Protein
chimera of homing endonuclease I-DmoI and DNA endonuclease I-CreI


Mass: 30025.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The chimera contains large domain of I-DmoI fused to one subunit of I-CreI: E-DreI protein
Source: (gene. exp.) Desulfurococcus mobilis (archaea), (gene. exp.) Chlamydomonas reinhardtii (plant)
Genus: Desulfurococcus, Chlamydomonas / Species: , / Strain: , / Plasmid: pDre16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]
References: UniProt: p21505, UniProt: p05725, UniProt: P21505*PLUS, Hydrolases; Acting on ester bonds

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Non-polymers , 4 types, 488 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 4.04 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulphate, MES, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulphate11
2MES11
3MgCl211
4MgCl212
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.1-2.4 Mammonium sulfate1reservoir
2100 mM1reservoirpH6.5
310 mM1reservoirMgCl2
41

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 91595 / % possible obs: 99.9 % / Redundancy: 3 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.081
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 91688 / % possible obs: 99 % / Num. measured all: 305673

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E-DreI computational model; I-CreI/DNA complex (RCSB 1G9Z)

1g9z


Resolution: 2.4→19.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1748854.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 4592 5 %RANDOM
Rwork0.231 ---
obs-91595 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.5375 Å2 / ksol: 0.363178 e/Å3
Displacement parametersBiso mean: 69.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å22.26 Å20 Å2
2---2.62 Å20 Å2
3---5.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 3747 164 454 10717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it2.781.5
X-RAY DIFFRACTIONc_mcangle_it3.672
X-RAY DIFFRACTIONc_scbond_it27.332
X-RAY DIFFRACTIONc_scangle_it31.992.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 774 5.1 %
Rwork0.305 14512 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5GLYCEROL.PARAM
Refinement
*PLUS
Rfactor Rfree: 0.256 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1

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