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- PDB-5akm: THE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET D... -

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Basic information

Entry
Database: PDB / ID: 5akm
TitleTHE CRYSTAL STRUCTURE OF I-DMOI G20S IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF 2MM MG
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 / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES / X-RAY CRYSTALLOGRAPHY.
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. / Marcaida, M.J. / Redondo, P. / Marenchino, M. / D'Abramo, M. / Montoya, G. / Prieto, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold.
Authors: Molina, R. / Marcaida, M.J. / Redondo, P. / Marenchino, M. / Duchateau, P. / D'Abramo, M. / Montoya, G. / Prieto, J.
History
DepositionMar 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 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)115,97822
Polymers115,70415
Non-polymers2747
Water1,15364
1
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)38,6768
Polymers38,5685
Non-polymers1083
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-64.2 kcal/mol
Surface area13810 Å2
MethodPISA
2
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)38,5926
Polymers38,5685
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-45.4 kcal/mol
Surface area14150 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)38,7108
Polymers38,5685
Non-polymers1423
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-48 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.390, 68.650, 107.340
Angle α, β, γ (deg.)90.00, 119.94, 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


Mass: 23295.084 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFUROCOCCUS MOBILIS (archaea) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / 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, 71 molecules

#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.04 Å3/Da / Density % sol: 60 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 97825 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 41.84 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 91.3

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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→46.528 Å / SU ML: 0.3 / σ(F): 0.96 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 4883 5 %
Rwork0.1792 --
obs0.1819 97689 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 3063 16 64 7572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077981
X-RAY DIFFRACTIONf_angle_d1.28711400
X-RAY DIFFRACTIONf_dihedral_angle_d23.6913207
X-RAY DIFFRACTIONf_chiral_restr0.0681284
X-RAY DIFFRACTIONf_plane_restr0.005910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42720.337970.31161802X-RAY DIFFRACTION55
2.4272-2.45580.35361750.28163258X-RAY DIFFRACTION95
2.4558-2.48570.30851570.26783009X-RAY DIFFRACTION95
2.4857-2.51720.28621660.25453164X-RAY DIFFRACTION96
2.5172-2.55030.31161750.2523245X-RAY DIFFRACTION96
2.5503-2.58530.30231620.23243030X-RAY DIFFRACTION96
2.5853-2.62220.29841650.2313162X-RAY DIFFRACTION96
2.6222-2.66130.27941610.24313160X-RAY DIFFRACTION96
2.6613-2.70290.30061600.24573104X-RAY DIFFRACTION95
2.7029-2.74720.34271690.24333153X-RAY DIFFRACTION95
2.7472-2.79460.25681570.22562995X-RAY DIFFRACTION94
2.7946-2.84540.31281680.23213170X-RAY DIFFRACTION94
2.8454-2.90010.30451710.22933203X-RAY DIFFRACTION96
2.9001-2.95930.2611690.21413215X-RAY DIFFRACTION97
2.9593-3.02360.34221620.21533089X-RAY DIFFRACTION96
3.0236-3.09390.23891690.20073189X-RAY DIFFRACTION96
3.0939-3.17130.23071660.19013148X-RAY DIFFRACTION96
3.1713-3.2570.24331720.18483256X-RAY DIFFRACTION96
3.257-3.35280.25231690.16593189X-RAY DIFFRACTION96
3.3528-3.4610.23341670.16773090X-RAY DIFFRACTION96
3.461-3.58470.2341520.16163057X-RAY DIFFRACTION94
3.5847-3.72820.22481590.17593082X-RAY DIFFRACTION94
3.7282-3.89770.23431660.17383181X-RAY DIFFRACTION96
3.8977-4.10310.21441660.15733157X-RAY DIFFRACTION96
4.1031-4.360.16831630.13843116X-RAY DIFFRACTION95
4.36-4.69640.21821670.1433155X-RAY DIFFRACTION96
4.6964-5.16840.22351600.14713087X-RAY DIFFRACTION94
5.1684-5.9150.18671600.15623048X-RAY DIFFRACTION94
5.915-7.44740.20491710.15933208X-RAY DIFFRACTION96
7.4474-46.53710.15911620.13813084X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 30.3411 Å / Origin y: -0.6391 Å / Origin z: 4.7085 Å
111213212223313233
T0.2861 Å2-0.0016 Å20.0026 Å2-0.2123 Å2-0.0365 Å2--0.3074 Å2
L0.8698 °20.0331 °2-0.0724 °2-0.3953 °2-0.146 °2--0.2307 °2
S0.0042 Å °-0.0338 Å °0.0096 Å °0.0049 Å °-0.0118 Å °0.0369 Å °-0.0599 Å °-0.0534 Å °0.0132 Å °
Refinement TLS groupSelection details: ALL

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