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- PDB-5o6i: Structures and dynamics of mesophilic variants from the homing en... -

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Basic information

Entry
Database: PDB / ID: 5o6i
TitleStructures and dynamics of mesophilic variants from the homing endonuclease I-DmoI
Components
  • (DNA (25-MER)) x 2
  • Homing endonuclease I-DmoI
KeywordsDNA BINDING PROTEIN / Desulfurococcus mobilis
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
LAGLIDADG-like domain / Intein / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Homing endonuclease I-DmoI
Similarity search - Component
Biological speciesDesulfurococcus mucosus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMolina, R. / Marcaida, M.J.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2017
Title: Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.
Authors: Alba, J. / Marcaida, M.J. / Prieto, J. / Montoya, G. / Molina, R. / D'Abramo, M.
History
DepositionJun 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / reflns_shell / Item: _citation.country
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homing endonuclease I-DmoI
C: DNA (25-MER)
D: DNA (25-MER)
F: Homing endonuclease I-DmoI
G: DNA (25-MER)
I: DNA (25-MER)
K: Homing endonuclease I-DmoI
L: DNA (25-MER)
N: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,73817
Polymers116,3379
Non-polymers4018
Water5,098283
1
A: Homing endonuclease I-DmoI
C: DNA (25-MER)
D: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9246
Polymers38,7793
Non-polymers1453
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-70 kcal/mol
Surface area14260 Å2
MethodPISA
2
F: Homing endonuclease I-DmoI
G: DNA (25-MER)
I: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9246
Polymers38,7793
Non-polymers1453
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-64 kcal/mol
Surface area14120 Å2
MethodPISA
3
K: Homing endonuclease I-DmoI
L: DNA (25-MER)
N: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8895
Polymers38,7793
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-57 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.000, 70.480, 107.320
Angle α, β, γ (deg.)90.00, 119.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules AFK

#1: Protein Homing endonuclease I-DmoI


Mass: 23416.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfurococcus mucosus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: P21505, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 6 molecules CGLDIN

#2: DNA chain DNA (25-MER)


Mass: 7707.932 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (25-MER)


Mass: 7654.926 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 291 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5-6 % PEG4000, 0.07 M NaAc pH = 4.6-5.5 and 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→56.14 Å / Num. obs: 64736 / % possible obs: 98 % / Redundancy: 5.2 % / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UN8

4un8


Resolution: 2.25→56.137 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 3282 5.07 %
Rwork0.1961 --
obs0.1977 64736 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→56.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 3057 8 283 7881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038146
X-RAY DIFFRACTIONf_angle_d0.60711643
X-RAY DIFFRACTIONf_dihedral_angle_d21.774361
X-RAY DIFFRACTIONf_chiral_restr0.0391311
X-RAY DIFFRACTIONf_plane_restr0.002942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.28360.34481500.28862696X-RAY DIFFRACTION99
2.2836-2.31930.32741390.27632603X-RAY DIFFRACTION99
2.3193-2.35730.33211560.28212704X-RAY DIFFRACTION99
2.3573-2.3980.31561540.27142624X-RAY DIFFRACTION99
2.398-2.44160.34391360.27722692X-RAY DIFFRACTION98
2.4416-2.48850.29331320.26662666X-RAY DIFFRACTION98
2.4885-2.53930.33251240.25582684X-RAY DIFFRACTION99
2.5393-2.59450.26581290.25012684X-RAY DIFFRACTION99
2.5945-2.65490.31761460.23592672X-RAY DIFFRACTION98
2.6549-2.72130.26241530.24332716X-RAY DIFFRACTION99
2.7213-2.79490.30521550.23452657X-RAY DIFFRACTION99
2.7949-2.87710.23871270.23412700X-RAY DIFFRACTION99
2.8771-2.970.28421450.22882716X-RAY DIFFRACTION99
2.97-3.07610.2681530.23542715X-RAY DIFFRACTION99
3.0761-3.19920.26021410.22352702X-RAY DIFFRACTION99
3.1992-3.34480.23741420.18882686X-RAY DIFFRACTION99
3.3448-3.52120.19971410.17662686X-RAY DIFFRACTION99
3.5212-3.74170.22891380.17492707X-RAY DIFFRACTION99
3.7417-4.03050.20491660.17592683X-RAY DIFFRACTION98
4.0305-4.4360.15611490.162667X-RAY DIFFRACTION96
4.436-5.07750.1961310.15752535X-RAY DIFFRACTION93
5.0775-6.39570.19241320.1672684X-RAY DIFFRACTION96
6.3957-56.15420.16791430.15972575X-RAY DIFFRACTION91

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