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- PDB-4una: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT... -

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Basic information

Entry
Database: PDB / ID: 4una
TitleTHE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 2 DAYS INCUBATION IN 5MM MN (STATE 4)
Components
  • 25MER
  • 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
  • 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
  • HOMING ENDONUCLEASE I-DMOI
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / CATALYSIS / PROTEIN-DNA INTERACTION
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 MOBILIS (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMolina, R. / Stella, S. / Redondo, P. / Gomez, H. / Marcaida, M.J. / Orozco, M. / Prieto, J. / Montoya, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease.
Authors: Molina, R. / Stella, S. / Redondo, P. / Gomez, H. / Marcaida, M.J. / Orozco, M. / Prieto, J. / Montoya, G.
History
DepositionMay 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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
A: HOMING ENDONUCLEASE I-DMOI
B: 25MER
C: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
D: HOMING ENDONUCLEASE I-DMOI
E: 25MER
F: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
G: HOMING ENDONUCLEASE I-DMOI
H: 25MER
I: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
K: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
M: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,24321
Polymers115,74912
Non-polymers4949
Water2,144119
1
A: HOMING ENDONUCLEASE I-DMOI
B: 25MER
C: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
K: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7487
Polymers38,5834
Non-polymers1653
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-63.3 kcal/mol
Surface area14120 Å2
MethodPISA
2
G: HOMING ENDONUCLEASE I-DMOI
H: 25MER
I: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7487
Polymers38,5834
Non-polymers1653
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-63.6 kcal/mol
Surface area13890 Å2
MethodPISA
3
D: HOMING ENDONUCLEASE I-DMOI
E: 25MER
F: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
M: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7487
Polymers38,5834
Non-polymers1653
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-66 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.517, 70.153, 106.704
Angle α, β, γ (deg.)90.00, 119.83, 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 / I-DMOI


Mass: 23265.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFUROCOCCUS MOBILIS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: P21505, Hydrolases; Acting on ester bonds

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DNA chain , 3 types, 9 molecules BEHCFIKMO

#2: DNA chain 25MER


Mass: 7707.932 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'


Mass: 4554.962 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'


Mass: 3055.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 128 molecules

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


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.31 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6 / Details: PH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.65
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65 Å / Relative weight: 1
ReflectionResolution: 2.3→46.28 Å / Num. obs: 261170 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 54.33 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 79.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VS7

2vs7


Resolution: 2.3→46.285 Å / SU ML: 0.31 / σ(F): 1.18 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 3841 3.4 %
Rwork0.1898 --
obs0.1908 113470 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4491 3060 9 119 7679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018034
X-RAY DIFFRACTIONf_angle_d1.19411476
X-RAY DIFFRACTIONf_dihedral_angle_d24.2213241
X-RAY DIFFRACTIONf_chiral_restr0.0561293
X-RAY DIFFRACTIONf_plane_restr0.007945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32910.3712890.33252851X-RAY DIFFRACTION66
2.3291-2.35980.35631180.32093114X-RAY DIFFRACTION73
2.3598-2.39210.32451080.30683251X-RAY DIFFRACTION77
2.3921-2.42630.33561430.30063622X-RAY DIFFRACTION84
2.4263-2.46250.3241400.29113885X-RAY DIFFRACTION91
2.4625-2.50090.29081510.28094201X-RAY DIFFRACTION98
2.5009-2.54190.30081520.26964151X-RAY DIFFRACTION99
2.5419-2.58580.34191510.26944230X-RAY DIFFRACTION99
2.5858-2.63280.29381380.2514214X-RAY DIFFRACTION99
2.6328-2.68340.29451660.26334210X-RAY DIFFRACTION99
2.6834-2.73820.32971340.24854244X-RAY DIFFRACTION99
2.7382-2.79770.28941500.24124269X-RAY DIFFRACTION99
2.7977-2.86280.29691480.23394119X-RAY DIFFRACTION99
2.8628-2.93440.30221490.22664245X-RAY DIFFRACTION99
2.9344-3.01370.29631320.22634213X-RAY DIFFRACTION99
3.0137-3.10240.27671520.21084269X-RAY DIFFRACTION99
3.1024-3.20250.21591510.20184293X-RAY DIFFRACTION99
3.2025-3.31690.25241540.18294144X-RAY DIFFRACTION99
3.3169-3.44970.2091640.18044272X-RAY DIFFRACTION99
3.4497-3.60660.21371450.17834132X-RAY DIFFRACTION100
3.6066-3.79670.22411220.1844337X-RAY DIFFRACTION100
3.7967-4.03440.21631600.18514167X-RAY DIFFRACTION99
4.0344-4.34570.21061360.16224220X-RAY DIFFRACTION99
4.3457-4.78260.1881450.15474271X-RAY DIFFRACTION100
4.7826-5.47370.17971520.1584263X-RAY DIFFRACTION99
5.4737-6.89270.12761470.1714162X-RAY DIFFRACTION99
6.8927-46.29430.17081440.15494280X-RAY DIFFRACTION99

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