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

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Basic information

Entry
Database: PDB / ID: 4unc
TitleTHE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8 DAYS INCUBATION IN 5MM MN (STATE 6)
Components
  • 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'
  • 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'
  • 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-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: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'
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: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'
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: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'
I: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
J: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'
K: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
L: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'
M: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
N: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,10824
Polymers115,61415
Non-polymers4949
Water2,126118
1
D: HOMING ENDONUCLEASE I-DMOI
E: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'
F: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
L: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'
M: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7038
Polymers38,5385
Non-polymers1653
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-63.5 kcal/mol
Surface area14550 Å2
MethodPISA
2
A: HOMING ENDONUCLEASE I-DMOI
B: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'
C: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
J: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'
K: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7038
Polymers38,5385
Non-polymers1653
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-64 kcal/mol
Surface area14150 Å2
MethodPISA
3
G: HOMING ENDONUCLEASE I-DMOI
H: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3'
I: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3'
N: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7038
Polymers38,5385
Non-polymers1653
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-61.2 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.803, 70.409, 107.172
Angle α, β, γ (deg.)90.00, 119.77, 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 , 4 types, 12 molecules BEHCFIJLNKMO

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


Mass: 4296.791 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(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3'


Mass: 3366.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: 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, 127 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 118 / 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→46.51 Å / Num. obs: 58967 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 52.27 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 92.2

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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 2VS8

2vs8


Resolution: 2.3→46.273 Å / SU ML: 0.29 / σ(F): 0.08 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 3968 3.4 %
Rwork0.1847 --
obs0.186 58929 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 3063 9 118 7713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098111
X-RAY DIFFRACTIONf_angle_d1.14411588
X-RAY DIFFRACTIONf_dihedral_angle_d23.7123269
X-RAY DIFFRACTIONf_chiral_restr0.0491306
X-RAY DIFFRACTIONf_plane_restr0.006960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32810.30871310.25873830X-RAY DIFFRACTION90
2.3281-2.35760.28011330.25843767X-RAY DIFFRACTION92
2.3576-2.38860.36491460.26443852X-RAY DIFFRACTION93
2.3886-2.42130.35171400.25383932X-RAY DIFFRACTION93
2.4213-2.45590.33051340.26183797X-RAY DIFFRACTION93
2.4559-2.49250.31311360.25283910X-RAY DIFFRACTION94
2.4925-2.53150.25841240.24113917X-RAY DIFFRACTION94
2.5315-2.5730.26611470.24463908X-RAY DIFFRACTION94
2.573-2.61730.3021530.23543969X-RAY DIFFRACTION94
2.6173-2.66490.30611360.2423859X-RAY DIFFRACTION95
2.6649-2.71620.29021280.24624033X-RAY DIFFRACTION96
2.7162-2.77160.31341420.24023904X-RAY DIFFRACTION95
2.7716-2.83190.28871360.23944014X-RAY DIFFRACTION96
2.8319-2.89770.25741580.23124002X-RAY DIFFRACTION96
2.8977-2.97020.28121340.22953948X-RAY DIFFRACTION96
2.9702-3.05050.23381520.21934107X-RAY DIFFRACTION97
3.0505-3.14020.26941330.19873945X-RAY DIFFRACTION97
3.1402-3.24160.2451470.19483998X-RAY DIFFRACTION97
3.2416-3.35740.22691290.19024065X-RAY DIFFRACTION97
3.3574-3.49180.22171400.1783990X-RAY DIFFRACTION97
3.4918-3.65060.2411530.17474064X-RAY DIFFRACTION98
3.6506-3.8430.22291550.1854050X-RAY DIFFRACTION98
3.843-4.08370.16551500.17644026X-RAY DIFFRACTION98
4.0837-4.39870.20071500.15514138X-RAY DIFFRACTION98
4.3987-4.8410.20451330.15484059X-RAY DIFFRACTION98
4.841-5.54050.19831430.16174129X-RAY DIFFRACTION99
5.5405-6.97660.22021480.15834082X-RAY DIFFRACTION99
6.9766-46.28220.14641570.13834127X-RAY DIFFRACTION99

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