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- PDB-1evw: L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMIN... -

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Basic information

Entry
Database: PDB / ID: 1evw
TitleL116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.
Components
  • DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
  • DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3')
  • DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3')
  • I-PPOI HOMING ENDONUCLEASE
KeywordsHydrolase/DNA / DNA binding B-sheets / C-terminal exchanged dimer interface / bent DNA / 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 / 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 / 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 / Resolution: 3.1 Å
AuthorsGalburt, E.A. / Jurica, M.S. / Chevalier, B.S. / Erho, D. / Stoddard, B.L.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.
Authors: Galburt, E.A. / Chadsey, M.S. / Jurica, M.S. / Chevalier, B.S. / Erho, D. / Tang, W. / Monnat Jr., R.J. / Stoddard, B.L.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3')
M: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
F: DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
O: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3')
G: DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3')
N: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
H: DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
P: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3')
A: I-PPOI HOMING ENDONUCLEASE
B: I-PPOI HOMING ENDONUCLEASE
C: I-PPOI HOMING ENDONUCLEASE
D: I-PPOI HOMING ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,05124
Polymers95,43112
Non-polymers62012
Water00
1
E: DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3')
M: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
F: DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
O: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3')
A: I-PPOI HOMING ENDONUCLEASE
B: I-PPOI HOMING ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,02612
Polymers47,7156
Non-polymers3106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3')
N: DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')
H: DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')
P: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3')
C: I-PPOI HOMING ENDONUCLEASE
D: I-PPOI HOMING ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,02612
Polymers47,7156
Non-polymers3106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.000, 73.100, 92.700
Angle α, β, γ (deg.)90.00, 95.40, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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DNA chain , 4 types, 8 molecules EGMNFHOP

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


Mass: 3637.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: sequence correspons to I-PpoI's homing site
#2: DNA chain DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3')


Mass: 2475.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: sequence correspons to I-PpoI's homing site
#3: DNA chain DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3')


Mass: 3612.378 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3')


Mass: 2451.630 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABCD

#5: Protein
I-PPOI HOMING ENDONUCLEASE / I-PPOI / INTRON-ENCODED ENDONUCLEASE I-PPOI


Mass: 17769.162 Da / Num. of mol.: 4 / Mutation: L116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94702

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Non-polymers , 2 types, 12 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, MES pH 6.5, NaCl, MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2NaCl11
3MgCl211
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
2200 mMammonium sulfate1reservoir
318 %PEG80001reservoir
4100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 19707 / Num. obs: 19707 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.4
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.238 / % possible all: 63.4
Reflection shell
*PLUS
% possible obs: 63.4 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1182 6 %random
Rwork0.273 ---
all-19707 --
obs-19707 --
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 1632 12 0 6612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_torsion_impr_deg0.86
X-RAY DIFFRACTIONx_torsion_deg28.2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.86

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