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- PDB-1ipp: HOMING ENDONUCLEASE/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ipp
TitleHOMING ENDONUCLEASE/DNA COMPLEX
Components
  • DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3')
  • INTRON-ENCODED ENDONUCLEASE I-PPOI
KeywordsTRANSCRIPTION/DNA / HOMING ENDONUCLEASE / INTRON / ZINC / DNA BINDING / PROTEIN FOLDING / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


intron homing / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A / Zinc-binding loop region of homing endonuclease / Homing endonuclease, His-Me finger superfamily / Zinc-binding loop region of homing endonuclease / Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A / His-Me finger superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Intron-encoded endonuclease I-PpoI
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsFlick, K.E. / Jurica, M.S. / Monnat Jr., R.J. / Stoddard, B.L.
Citation
Journal: Nature / Year: 1998
Title: DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Authors: Flick, K.E. / Jurica, M.S. / Monnat Jr., R.J. / Stoddard, B.L.
#1: Journal: Protein Sci. / Year: 1997
Title: Crystallization and Preliminary X-Ray Studies of I-Ppoi: A Nuclear, Intron- Encoded Homing Endonuclease from Physarum Polycephalum
Authors: Flick, K.E. / Mchugh, D. / Heath, J.D. / Stephens, K.M. / Monnat Jr., R.J. / Stoddard, B.L.
History
DepositionMar 19, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 2, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,99510
Polymers48,4974
Non-polymers4986
Water9,854547
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.900, 113.900, 88.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.970715, 0.239393, 0.020068), (0.239758, 0.970659, 0.018334), (-0.01509, 0.022609, -0.99963)
Vector: 26.7677, -3.8749, 57.6715)

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Components

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


Mass: 6437.184 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein INTRON-ENCODED ENDONUCLEASE I-PPOI


Mass: 17811.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Cellular location: NUCLEUSCell nucleus / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q94702
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDA 213 IN CHAINS C AND D ARE THE SITES OF ENDONUCLEASE CLEAVAGE

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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: 3.4 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion / pH: 5.4
Details: THE CRYSTALS WERE GROWN FROM A 2:1 MOLAR RATIO SOLUTION OF PROTEIN AND DNA SUPPLEMENTED WITH 2.5 MM EDTA AND 5 MM SPERMINE. THE COMPLEX WAS CRYSTALLIZED FROM 21 - 27% PEG 4000, 0.1 M ...Details: THE CRYSTALS WERE GROWN FROM A 2:1 MOLAR RATIO SOLUTION OF PROTEIN AND DNA SUPPLEMENTED WITH 2.5 MM EDTA AND 5 MM SPERMINE. THE COMPLEX WAS CRYSTALLIZED FROM 21 - 27% PEG 4000, 0.1 M CITRATE, PH 5.4 - 5.8; 20 MM NACL, 2 MM EDTA., VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1EDTAEthylenediaminetetraacetic acid11
2SPERMINE11
3NACLSodium chloride11
4SODIUM CITRATE11
5PEG 400011
6PEG 400012
7SODIUM CITRATE12
8NACLSodium chloride12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: DNA:protein solution(in 2:1 ratio) was mixed with an equal volume of reservoir solution
PH range low: 5.6 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlI-PpoI1drop
220 mM1reservoirNaCl
32 mMEDTA1reservoir
40.1 Mcitrate1reservoir
521-27 %PEG40001reservoir
61
71
81

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: NONE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30702 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.048 / Rsym value: 4.8 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.7 / Rsym value: 19.3 / % possible all: 41
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Num. measured all: 83203
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.24 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1564 5 %RANDOM
Rwork0.212 ---
obs-30671 90.2 %-
Displacement parametersBiso mean: 31.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 856 6 547 3899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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: 2.2→2.31 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.423 85 4.5 %
Rwork0.33 1871 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.33

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