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- PDB-4d6n: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT... -

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Basic information

Entry
Database: PDB / ID: 4d6n
TitleTHE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 10 DAYS INCUBATION IN 5MM MG (STATE 7)
Components
  • 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
  • 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3'
  • 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'
  • 5'-D(*DGP*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: 2.35 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
DepositionNov 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 2023Group: 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(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'
C: 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
D: 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3'
E: 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
F: HOMING ENDONUCLEASE I-DMOI
G: 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'
H: 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
I: 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3'
J: 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
K: HOMING ENDONUCLEASE I-DMOI
L: 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'
M: 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
N: 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3'
O: 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,93724
Polymers115,61415
Non-polymers3239
Water3,009167
1
K: HOMING ENDONUCLEASE I-DMOI
L: 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'
M: 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
N: 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3'
O: 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5877
Polymers38,5385
Non-polymers492
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-59.5 kcal/mol
Surface area13920 Å2
MethodPISA
2
F: HOMING ENDONUCLEASE I-DMOI
G: 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'
H: 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
I: 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3'
J: 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6468
Polymers38,5385
Non-polymers1083
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-62.5 kcal/mol
Surface area14170 Å2
MethodPISA
3
A: HOMING ENDONUCLEASE I-DMOI
B: 5'-D(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3'
C: 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
D: 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3'
E: 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7059
Polymers38,5385
Non-polymers1674
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-62 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.311, 70.269, 107.169
Angle α, β, γ (deg.)90.00, 119.59, 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(*DGP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*DAP)-3' / 14MER


Mass: 4296.791 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*DGP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3' / 11MER


Mass: 3366.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*DCP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*DAP*C)-3' / 15MER


Mass: 4554.962 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: DNA chain 5'-D(*DCP*CP*GP*GP*CP*AP*AP*GP*GP*CP)-3' / 10MER


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, 176 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#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.: 167 / 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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→46.6 Å / Num. obs: 56760 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 49.85 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.6
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

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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: 2.35→46.598 Å / SU ML: 0.27 / σ(F): 0.07 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 3928 3.5 %
Rwork0.1824 --
obs0.1836 56723 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→46.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 3063 18 167 7782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098101
X-RAY DIFFRACTIONf_angle_d1.22811570
X-RAY DIFFRACTIONf_dihedral_angle_d24.3313245
X-RAY DIFFRACTIONf_chiral_restr0.061302
X-RAY DIFFRACTIONf_plane_restr0.007934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37870.34421340.28393803X-RAY DIFFRACTION98
2.3787-2.40880.33791440.27533842X-RAY DIFFRACTION99
2.4088-2.44050.35091350.27333800X-RAY DIFFRACTION98
2.4405-2.47390.29211370.26383795X-RAY DIFFRACTION99
2.4739-2.50920.29811280.25063892X-RAY DIFFRACTION99
2.5092-2.54670.3151380.23883795X-RAY DIFFRACTION99
2.5467-2.58650.2931500.22733790X-RAY DIFFRACTION99
2.5865-2.62890.25921420.23073851X-RAY DIFFRACTION99
2.6289-2.67420.27111500.233807X-RAY DIFFRACTION99
2.6742-2.72280.2511260.22753892X-RAY DIFFRACTION99
2.7228-2.77520.33891400.2393702X-RAY DIFFRACTION99
2.7752-2.83180.28661450.24053783X-RAY DIFFRACTION96
2.8318-2.89340.30311270.22963855X-RAY DIFFRACTION99
2.8934-2.96070.2811540.22393796X-RAY DIFFRACTION99
2.9607-3.03470.26571500.21593885X-RAY DIFFRACTION99
3.0347-3.11670.22661310.20543793X-RAY DIFFRACTION99
3.1167-3.20840.21421440.20533841X-RAY DIFFRACTION99
3.2084-3.3120.22141460.18463803X-RAY DIFFRACTION99
3.312-3.43030.22431420.19113846X-RAY DIFFRACTION99
3.4303-3.56760.1951420.17673839X-RAY DIFFRACTION99
3.5676-3.72990.20731300.1953736X-RAY DIFFRACTION97
3.7299-3.92650.16931380.17743902X-RAY DIFFRACTION100
3.9265-4.17230.20421350.16323840X-RAY DIFFRACTION100
4.1723-4.49420.18751400.14913841X-RAY DIFFRACTION100
4.4942-4.94610.18621540.15473887X-RAY DIFFRACTION100
4.9461-5.66070.2021410.15983745X-RAY DIFFRACTION97
5.6607-7.12780.19081500.15213874X-RAY DIFFRACTION100
7.1278-46.60710.15861350.12953800X-RAY DIFFRACTION99

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