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- PDB-4un8: THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT... -

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Basic information

Entry
Database: PDB / ID: 4un8
TitleTHE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2)
Components
  • (25MER) x 2
  • (HOMING ENDONUCLEASE I- ...) x 2
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / DNA-BINDING PROTEIN / 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: 2.6 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: 25MER
D: HOMING ENDONUCLEASE I-DMOI
E: 25MER
F: 25MER
G: HOMING ENDONUCLEASE I-DMOI
H: 25MER
I: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,22815
Polymers115,8999
Non-polymers3306
Water2,846158
1
D: HOMING ENDONUCLEASE I-DMOI
E: 25MER
F: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7385
Polymers38,6283
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-58.1 kcal/mol
Surface area14370 Å2
MethodPISA
2
G: HOMING ENDONUCLEASE I-DMOI
H: 25MER
I: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7535
Polymers38,6433
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-53.7 kcal/mol
Surface area13930 Å2
MethodPISA
3
A: HOMING ENDONUCLEASE I-DMOI
B: 25MER
C: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7385
Polymers38,6283
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-53.6 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.186, 70.851, 107.232
Angle α, β, γ (deg.)90.00, 119.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HOMING ENDONUCLEASE I- ... , 2 types, 3 molecules ADG

#1: Protein HOMING ENDONUCLEASE I-DMOI


Mass: 23265.057 Da / Num. of mol.: 2
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
#4: Protein HOMING ENDONUCLEASE I-DMOI


Mass: 23280.068 Da / Num. of mol.: 1
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 , 2 types, 6 molecules BEHCFI

#2: DNA chain 25MER


Mass: 7707.932 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 25MER


Mass: 7654.926 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 164 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.36 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: 2.6→46.64 Å / Num. obs: 42078 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 52.87 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 95.6

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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: 2.6→46.642 Å / SU ML: 0.32 / σ(F): 1.12 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 3892 4.8 %
Rwork0.1784 --
obs0.1806 42060 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→46.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 3057 6 158 7772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018162
X-RAY DIFFRACTIONf_angle_d1.21211665
X-RAY DIFFRACTIONf_dihedral_angle_d23.6713310
X-RAY DIFFRACTIONf_chiral_restr0.0531310
X-RAY DIFFRACTIONf_plane_restr0.006973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63170.33151420.27332804X-RAY DIFFRACTION95
2.6317-2.6650.29221310.2642662X-RAY DIFFRACTION95
2.665-2.70010.35611320.2632794X-RAY DIFFRACTION95
2.7001-2.73710.27571290.25282794X-RAY DIFFRACTION95
2.7371-2.77620.28581410.24852634X-RAY DIFFRACTION95
2.7762-2.81760.291310.23732736X-RAY DIFFRACTION94
2.8176-2.86160.26181460.22092719X-RAY DIFFRACTION95
2.8616-2.90850.25421460.21072712X-RAY DIFFRACTION95
2.9085-2.95870.26171290.2042752X-RAY DIFFRACTION96
2.9587-3.01250.29581340.20352790X-RAY DIFFRACTION97
3.0125-3.07040.25071340.20942800X-RAY DIFFRACTION96
3.0704-3.13310.28381460.1922754X-RAY DIFFRACTION97
3.1331-3.20120.23091400.19012747X-RAY DIFFRACTION97
3.2012-3.27560.21621450.16732738X-RAY DIFFRACTION96
3.2756-3.35750.21621440.16132761X-RAY DIFFRACTION95
3.3575-3.44830.17431190.14642728X-RAY DIFFRACTION95
3.4483-3.54970.16751300.15512803X-RAY DIFFRACTION97
3.5497-3.66420.19461440.16122785X-RAY DIFFRACTION98
3.6642-3.79510.24911360.17182784X-RAY DIFFRACTION97
3.7951-3.9470.22261540.17452808X-RAY DIFFRACTION98
3.947-4.12650.20791470.17262827X-RAY DIFFRACTION97
4.1265-4.3440.22141360.16022717X-RAY DIFFRACTION96
4.344-4.61590.22131470.16232767X-RAY DIFFRACTION96
4.6159-4.97190.23331420.16542825X-RAY DIFFRACTION99
4.9719-5.47160.2451290.17632817X-RAY DIFFRACTION98
5.4716-6.26170.23931390.17372786X-RAY DIFFRACTION97
6.2617-7.88290.18091340.18542821X-RAY DIFFRACTION98
7.8829-46.64940.16811650.15892721X-RAY DIFFRACTION96

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