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- PDB-1a73: INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1a73
TitleINTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA
Components
  • DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
  • DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
  • INTRON 3 (I-PPO) ENCODED ENDONUCLEASE
KeywordsHYDROLASE/DNA / COMPLEX (HOMING ENDONUCLEASE-DNA) / INTRON / ZINC / DNA BINDING / PROTEIN FOLDING / HYDROLASE-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 / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsFlick, K.E. / Monnat Junior, 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 Junior, R.J. / Stoddard, B.L.
History
DepositionMar 19, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 14, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / software / 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 / _software.name / _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*A)-3')
D: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
E: DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
F: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
A: INTRON 3 (I-PPO) ENCODED ENDONUCLEASE
B: INTRON 3 (I-PPO) ENCODED ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,71712
Polymers48,4076
Non-polymers3106
Water7,044391
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.700, 113.700, 88.400
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

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DNA chain , 2 types, 4 molecules CEDF

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


Mass: 3916.571 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE I-PPOI BINDING SEQUENCE / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')


Mass: 2475.655 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE I-PPOI BINDING SEQUENCE / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein INTRON 3 (I-PPO) ENCODED ENDONUCLEASE / INTRON-ENCODED ENDONUCLEASE I-PPOI


Mass: 17811.242 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE (I-PPO) ENCODED ENDONUCLEASE
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

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Non-polymers , 3 types, 397 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsADENOSINES C 21 AND D 21 ARE 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, hanging drop / pH: 5.6
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., pH 5.6, VAPOR DIFFUSION, HANGING DROP
PH range: 5.4-5.8
Components of the solutions
IDNameCrystal-IDSol-ID
1EDTAEthylenediaminetetraacetic acid11
2SPERMINE11
3PEG 400011
4NACLSodium chloride11
5SODIUM CITRATE11
6PEG 400012
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃
Details: DNA:protein solution(in 2:1 ratio) was mixed with an equal volume of reservoir solution, Flick, K.E., (1997) Protein Sci., 6, 2677.
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC / Detector: CCD / Date: Dec 15, 1997 / Details: NONE
RadiationMonochromator: DOUBLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 362336 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.04 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.97 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.12 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 71892 / Num. measured all: 362336

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.297 3581 5 %RANDOM
Rwork0.208 ---
obs0.208 71629 99.4 %-
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 856 6 391 3743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.3
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: 1.8→1.87 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.412 352 5 %
Rwork0.336 7042 -
obs--99.4 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
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

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