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- PDB-2fld: I-MsoI Re-Designed for Altered DNA Cleavage Specificity -

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Basic information

Entry
Database: PDB / ID: 2fld
TitleI-MsoI Re-Designed for Altered DNA Cleavage Specificity
Components
  • 5'-D(*CP*GP*GP*AP*AP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*TP*TP*CP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*GP*AP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*TP*TP*CP*CP*G)-3'
  • DNA ENDONUCLEASE I-MSOI
KeywordsHYDROLASE/DNA / homing endonuclease / dna / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


chloroplast / endonuclease activity / metal ion binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Site-specific DNA endonuclease I-MsoI / :
Similarity search - Component
Biological speciesMonomastix sp. (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAshworth, J. / Duarte, C.M. / Havranek, J.J. / Sussman, D. / Monnat, R.J. / Stoddard, B.L. / Baker, D.
CitationJournal: Nature / Year: 2006
Title: Computational redesign of endonuclease DNA binding and cleavage specificity.
Authors: Ashworth, J. / Havranek, J.J. / Duarte, C.M. / Sussman, D. / Monnat, R.J. / Stoddard, B.L. / Baker, D.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Sep 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI ..._reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*AP*GP*AP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*TP*TP*CP*CP*G)-3'
D: 5'-D(*CP*GP*GP*AP*AP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*TP*TP*CP*TP*GP*C)-3'
A: DNA ENDONUCLEASE I-MSOI
B: DNA ENDONUCLEASE I-MSOI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7157
Polymers52,6124
Non-polymers1033
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.961, 42.981, 71.545
Angle α, β, γ (deg.)72.29, 72.30, 70.51
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 2 types, 2 molecules CD

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


Mass: 7435.791 Da / Num. of mol.: 1 / Mutation: L28K, R83T / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*GP*AP*AP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*TP*TP*CP*TP*GP*C)-3'


Mass: 7306.704 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein DNA ENDONUCLEASE I-MSOI


Mass: 18934.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monomastix sp. (plant) / Strain: OKE-1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8WKW7, UniProt: C0JWR6*PLUS

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Non-polymers , 3 types, 100 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 400, 100 mM Tris, 50 mM NaCl, 10 mM CaCl2, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K
Components of the solutions
IDNameCrystal-IDSol-ID
130% PEG 400, 100 mM Tris,50 mM NaCl, 10 mM CaCl211
230% PEG 400, 100 mM Tris,50 mM NaCl, 10 mM CaCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2005
RadiationMonochromator: single crystal, cylindrical ben / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.5 Å / Num. obs: 27855 / % possible obs: 94.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3 / % possible all: 74.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M5X, MUTATED RESIDUES EXCLUDED

1m5x


Resolution: 2→39.5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.271 1257 4.3 %
Rwork0.229 --
obs0.229 26086 88.3 %
all-54004 -
Solvent computationBsol: 25.02 Å2
Displacement parametersBiso mean: 38.12 Å2
Baniso -1Baniso -2Baniso -3
1--25.756 Å21.354 Å2-3.575 Å2
2--12.513 Å2-6.07 Å2
3---13.243 Å2
Refinement stepCycle: LAST / Resolution: 2→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 978 3 97 3711
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER.PARAM
X-RAY DIFFRACTION5WATER_REP.PARAM

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