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- PDB-4ut0: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT... -

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Basic information

Entry
Database: PDB / ID: 4ut0
TitleTHE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MN (STATE 7)
Components
  • 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
  • 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
  • 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
  • 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-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
ACETATE ION / : / DNA / DNA (> 10) / Homing endonuclease I-DmoI
Similarity search - Component
Biological speciesDESULFUROCOCCUS MOBILIS (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionJul 17, 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*AP)-3'
C: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
D: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
E: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
F: HOMING ENDONUCLEASE I-DMOI
G: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
H: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
I: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
J: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
K: HOMING ENDONUCLEASE I-DMOI
L: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
M: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
N: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,12124
Polymers115,61415
Non-polymers5079
Water1,820101
1
K: HOMING ENDONUCLEASE I-DMOI
L: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
M: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
N: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
O: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6487
Polymers38,5385
Non-polymers1102
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-54.4 kcal/mol
Surface area14010 Å2
MethodPISA
2
F: HOMING ENDONUCLEASE I-DMOI
G: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
H: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
I: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
J: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7078
Polymers38,5385
Non-polymers1693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-58.9 kcal/mol
Surface area14250 Å2
MethodPISA
3
A: HOMING ENDONUCLEASE I-DMOI
B: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
C: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
D: 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'
E: 5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7669
Polymers38,5385
Non-polymers2284
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-56.8 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.984, 70.387, 107.154
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 / 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 BGLCHMDINEJO

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


Mass: 4296.791 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'


Mass: 3366.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*CP)-3'


Mass: 4554.962 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*CP)-3'


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

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Non-polymers , 3 types, 110 molecules

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


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.33 Å3/Da / Density % sol: 53 % / 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: 2.4→46.49 Å / Num. obs: 54032 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 53.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 99

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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: 2.4→46.489 Å / SU ML: 0.31 / σ(F): 0.05 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 3877 3.7 %
Rwork0.1829 --
obs0.1845 53993 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 3063 18 101 7721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018106
X-RAY DIFFRACTIONf_angle_d1.26911577
X-RAY DIFFRACTIONf_dihedral_angle_d23.8773246
X-RAY DIFFRACTIONf_chiral_restr0.0681303
X-RAY DIFFRACTIONf_plane_restr0.007935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42930.3091430.27113685X-RAY DIFFRACTION99
2.4293-2.460.30741320.28523517X-RAY DIFFRACTION98
2.46-2.49240.37731560.27683645X-RAY DIFFRACTION99
2.4924-2.52650.35311420.27063582X-RAY DIFFRACTION100
2.5265-2.56260.33431400.26553673X-RAY DIFFRACTION100
2.5626-2.60090.32411500.25823645X-RAY DIFFRACTION100
2.6009-2.64150.26781440.26623556X-RAY DIFFRACTION99
2.6415-2.68480.34661440.26853716X-RAY DIFFRACTION99
2.6848-2.73110.31661320.2633575X-RAY DIFFRACTION99
2.7311-2.78080.39441340.24963621X-RAY DIFFRACTION99
2.7808-2.83420.26921160.24753623X-RAY DIFFRACTION99
2.8342-2.89210.26561410.23063614X-RAY DIFFRACTION98
2.8921-2.9550.30111320.2293599X-RAY DIFFRACTION99
2.955-3.02370.2851300.22513579X-RAY DIFFRACTION100
3.0237-3.09930.25721410.22533702X-RAY DIFFRACTION100
3.0993-3.18310.26571380.20953606X-RAY DIFFRACTION100
3.1831-3.27670.22781300.19313697X-RAY DIFFRACTION100
3.2767-3.38240.21191480.18453613X-RAY DIFFRACTION100
3.3824-3.50330.17951300.17463602X-RAY DIFFRACTION99
3.5033-3.64350.21771390.17643625X-RAY DIFFRACTION98
3.6435-3.80920.20291240.17973618X-RAY DIFFRACTION100
3.8092-4.010.2251320.17963732X-RAY DIFFRACTION100
4.01-4.26110.22641410.14993558X-RAY DIFFRACTION100
4.2611-4.58980.19811380.15073647X-RAY DIFFRACTION100
4.5898-5.05120.20241500.14923615X-RAY DIFFRACTION99
5.0512-5.78090.18171420.15723628X-RAY DIFFRACTION99
5.7809-7.27880.19281380.16143627X-RAY DIFFRACTION100
7.2788-46.49730.19171500.13373616X-RAY DIFFRACTION99

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