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- PDB-1n3e: Crystal structure of I-CreI bound to a palindromic DNA sequence I... -

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Basic information

Entry
Database: PDB / ID: 1n3e
TitleCrystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence)
Components
  • 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3'
  • 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3'
  • DNA endonuclease I-CreI
KeywordsHYDROLASE/DNA / Homing / endonuclease / LAGLIDADG / DNA recognition / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / 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) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChevalier, B. / Turmel, M. / Lemieux, C. / Monnat, R.J. / Stoddard, B.L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI
Authors: Chevalier, B. / Turmel, M. / Lemieux, C. / Monnat, R.J. / Stoddard, B.L.
History
DepositionOct 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE DEPOSITORS BELIEVE THAT THE SEQUENCE GIVEN IN SWISSPROTT ENTRY P05725 IS INCORRECT FOR ...SEQUENCE THE DEPOSITORS BELIEVE THAT THE SEQUENCE GIVEN IN SWISSPROTT ENTRY P05725 IS INCORRECT FOR RESIDUES 42, 110, 111.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,52222
Polymers104,18912
Non-polymers33210
Water4,197233
1
C: 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3'
D: 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3'
E: 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3'
F: 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3'
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26111
Polymers52,0956
Non-polymers1665
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3'
J: 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3'
K: 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3'
L: 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3'
G: DNA endonuclease I-CreI
H: DNA endonuclease I-CreI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26111
Polymers52,0956
Non-polymers1665
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.730, 68.440, 301.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 8 molecules CEIKDFJL

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


Mass: 4273.806 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3'


Mass: 3051.001 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABGH

#3: Protein
DNA endonuclease I-CreI / 23S rRNA intron protein


Mass: 18722.557 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CR.LSU INTRON OF CHOROPLAST 23S RDNA GENE / Plasmid: pI-CreI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]
References: UniProt: P05725, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 243 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.42 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 400, 20 mM NaCl, 10 mM CaCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2NaClSodium chloride11
3CaCl211
4MES11
512
6NaClSodium chloride12
7CaCl212
812

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.18 Å / Num. obs: 32395 / Biso Wilson estimate: 40.3 Å2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9Z

1g9z


Resolution: 2.5→46.18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1083871.21 / Data cutoff high rms absF: 1083871.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1598 4.9 %RANDOM
Rwork0.219 ---
obs0.219 32395 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.4874 Å2 / ksol: 0.301562 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--4.31 Å20 Å2
3----5.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 1960 10 233 7101
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 217 4.6 %
Rwork0.314 4451 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5

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