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- PDB-1bp7: GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING S... -

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Basic information

Entry
Database: PDB / ID: 1bp7
TitleGROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA
Components
  • DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3')
  • PROTEIN (I-CREI)
KeywordsTRANSCRIPTION/DNA / ENDONUCLEASE / GROUP I MOBILE INTRON / INTRON HOMING / CHLOROPLAST DNA / LAGLIDADG MOTIF / DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / identical protein 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJurica, M.S. / Monnat Junior, R.J. / Stoddard, B.L.
CitationJournal: Mol.Cell / Year: 1998
Title: DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI.
Authors: Jurica, M.S. / Monnat Jr., R.J. / Stoddard, B.L.
History
DepositionAug 13, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_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_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
1: DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3')
2: DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3')
3: DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3')
4: DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3')
A: PROTEIN (I-CREI)
B: PROTEIN (I-CREI)
C: PROTEIN (I-CREI)
D: PROTEIN (I-CREI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,70412
Polymers99,5448
Non-polymers1604
Water1267
1
1: DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3')
2: DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3')
A: PROTEIN (I-CREI)
B: PROTEIN (I-CREI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8526
Polymers49,7724
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
3: DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3')
4: DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3')
C: PROTEIN (I-CREI)
D: PROTEIN (I-CREI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8526
Polymers49,7724
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.556, 89.259, 177.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 7418.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 24 BASE PAIR DUPLEX DNA
#2: DNA chain DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3') / HOMING SITE


Mass: 7320.728 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 24 BASE PAIR DUPLEX DNA
#3: Protein
PROTEIN (I-CREI) / DNA ENDONUCLEASE I-CREI


Mass: 17516.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Organelle: CHLOROPLAST / Production host: Escherichia coli (E. coli) / References: UniProt: P05725
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.65 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5 / Details: pH 6.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2MES11
3CACL211
4NACL11
51-3-PROPANEDIOL11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
2DNA1drop2:1 molar ratio of DNA:protein
314 %PEG33501reservoir
4100 mMMES1reservoir
510 mM1reservoirCaCl2
620 mM1reservoirNaCl
70.2 %1-3 propanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. all: 86360 / Num. obs: 86360 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.12 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.297 / % possible all: 79.6
Reflection
*PLUS
Num. obs: 20643 / Num. measured all: 86360 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 79.6 % / Rmerge(I) obs: 0.297

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Processing

Software
NameVersionClassification
EPMRphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AF5 DIMER

1af5


Resolution: 3→100 Å / Rfactor Rfree error: 0.0081 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1202 6 %RANDOM
Rwork0.234 ---
all-20643 --
obs-20643 92.9 %-
Refinement stepCycle: LAST / Resolution: 3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4948 1956 4 7 6915
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_deg1.267
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.48
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.861
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3242 113 5.56 %
Rwork0.3125 1923 -
obs--75.13 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION3PARAMETER.ELEMENTSDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION4TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 100 Å / Rfactor obs: 0.242 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.322
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.48
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.861
LS refinement shell
*PLUS
Rfactor obs: 0.3125

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