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- PDB-2o6m: H98Q mutant of the homing endonuclease I-PPOI complexed with DNA -

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Basic information

Entry
Database: PDB / ID: 2o6m
TitleH98Q mutant of the homing endonuclease I-PPOI complexed with DNA
Components
  • 5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3'
  • Intron-encoded endonuclease I-PpoI
KeywordsHYDROLASE/DNA / HOMING ENDONUCLEASE / HOMODIMER / PROTEIN-DNA COMPLEX / HNH / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEastberg, J.H. / Stoddard, B.L.
CitationJournal: Biochemistry / Year: 2007
Title: Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.
Authors: Eastberg, J.H. / Eklund, J. / Monnat, R. / Stoddard, B.L.
History
DepositionDec 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3'
D: 5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3'
A: Intron-encoded endonuclease I-PpoI
B: Intron-encoded endonuclease I-PpoI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,78710
Polymers48,4774
Non-polymers3106
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.850, 113.850, 88.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain 5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3'


Mass: 6437.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: I-PpoI Binding Sequence
#2: Protein Intron-encoded endonuclease I-PpoI / I-Ppo


Mass: 17801.225 Da / Num. of mol.: 2 / Mutation: H98Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Gene: I-PpoI / Plasmid: pET-Ppo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Ril
References: UniProt: Q94702, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Citrate, pH 5.2-5.8, 20 mM NaCl, 2 mM EDTA, 20-30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Components of the solutions
IDNameCrystal-IDSol-ID
1Citrate11
2NaCl11
3EDTA11
4PEG 400011
5HOH11
6Citrate12
7NaCl12
8PEG 400012
9HOH12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2005
RadiationMonochromator: single crystal, cylindrical beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29954 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.5 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CYQ

1cyq


Resolution: 2.3→49.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 82877.617 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2880 10 %RANDOM
Rwork0.211 ---
all0.211 28703 --
obs0.211 28703 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.473 Å2 / ksol: 0.416 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20.11 Å20 Å2
2---2.79 Å20 Å2
3---5.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 854 6 286 3634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it3.161.5
X-RAY DIFFRACTIONc_mcangle_it4.92
X-RAY DIFFRACTIONc_scbond_it3.972
X-RAY DIFFRACTIONc_scangle_it5.472.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 458 10.6 %
Rwork0.247 3872 -
obs-4330 88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna.paramdna-rna.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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