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- PDB-5o6g: Structures and dynamics of mesophilic variants from the homing en... -

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Basic information

Entry
Database: PDB / ID: 5o6g
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: 2.75 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_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
B: DNA (25-MER)
C: DNA (25-MER)
D: Homing endonuclease I-DmoI
E: DNA (25-MER)
F: DNA (25-MER)
G: Homing endonuclease I-DmoI
H: DNA (25-MER)
I: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,78916
Polymers116,4249
Non-polymers3657
Water93752
1
A: Homing endonuclease I-DmoI
B: DNA (25-MER)
C: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9185
Polymers38,8083
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-56 kcal/mol
Surface area14100 Å2
MethodPISA
2
D: Homing endonuclease I-DmoI
E: DNA (25-MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9185
Polymers38,8083
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-54 kcal/mol
Surface area14030 Å2
MethodPISA
3
G: Homing endonuclease I-DmoI
H: DNA (25-MER)
I: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9536
Polymers38,8083
Non-polymers1453
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-64 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.280, 70.500, 107.150
Angle α, β, γ (deg.)90.00, 119.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ADG

#1: Protein Homing endonuclease I-DmoI


Mass: 23445.240 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 BEHCFI

#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, 59 molecules

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


Mass: 54.938 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 59.24 %
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 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: 2.75→93.1 Å / Num. obs: 35510 / % possible obs: 97.5 % / Redundancy: 4.7 % / Net I/σ(I): 9.4

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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: 2.75→56.184 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82
RfactorNum. reflection% reflection
Rfree0.2322 1995 5.62 %
Rwork0.1772 --
obs0.1803 35510 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→56.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 3057 7 52 7616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098079
X-RAY DIFFRACTIONf_angle_d1.14511544
X-RAY DIFFRACTIONf_dihedral_angle_d22.7034311
X-RAY DIFFRACTIONf_chiral_restr0.061293
X-RAY DIFFRACTIONf_plane_restr0.006930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81880.40521430.31482383X-RAY DIFFRACTION96
2.8188-2.8950.33811430.28542313X-RAY DIFFRACTION97
2.895-2.98020.30931420.24862384X-RAY DIFFRACTION98
2.9802-3.07640.32571320.22282388X-RAY DIFFRACTION97
3.0764-3.18630.28241380.1962335X-RAY DIFFRACTION97
3.1863-3.31390.24521400.18382385X-RAY DIFFRACTION98
3.3139-3.46470.2121460.17182433X-RAY DIFFRACTION98
3.4647-3.64730.25321490.15782381X-RAY DIFFRACTION98
3.6473-3.87580.21231430.1752400X-RAY DIFFRACTION98
3.8758-4.17490.23691420.16362392X-RAY DIFFRACTION97
4.1749-4.59490.20691420.14842395X-RAY DIFFRACTION98
4.5949-5.25940.19841360.15392411X-RAY DIFFRACTION98
5.2594-6.62460.19821490.17212433X-RAY DIFFRACTION98
6.6246-56.19570.20381500.16662482X-RAY DIFFRACTION97

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