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- PDB-5akf: THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TAR... -

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Basic information

Entry
Database: PDB / ID: 5akf
TitleTHE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA NICKED IN THE CODING STRAND A AND IN THE PRESENCE OF 2MM MN
Components
  • 25MER
  • 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
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: 2.45 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 3, 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: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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: 25MER
E: HOMING ENDONUCLEASE I-DMOI
F: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
G: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
H: 25MER
I: HOMING ENDONUCLEASE I-DMOI
J: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
K: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
L: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,94920
Polymers115,58412
Non-polymers3668
Water5,423301
1
I: HOMING ENDONUCLEASE I-DMOI
J: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
K: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
L: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6186
Polymers38,5284
Non-polymers902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-52.3 kcal/mol
Surface area13900 Å2
MethodPISA
2
E: HOMING ENDONUCLEASE I-DMOI
F: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
G: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3'
H: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6186
Polymers38,5284
Non-polymers902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-56.3 kcal/mol
Surface area13830 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: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7138
Polymers38,5284
Non-polymers1854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-65.4 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.820, 70.470, 107.100
Angle α, β, γ (deg.)90.00, 119.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules AEI

#1: Protein HOMING ENDONUCLEASE I-DMOI / I-DMOI


Mass: 23210.021 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 (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 , 3 types, 9 molecules BFJCGKDHL

#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 25MER


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

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Non-polymers , 4 types, 309 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.37 Å3/Da / Density % sol: 54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.8929
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8929 Å / Relative weight: 1
ReflectionResolution: 2.45→56.14 Å / Num. obs: 50841 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 51.72 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % 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: 2VS7

2vs7


Resolution: 2.45→42.65 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2564 5.1 %
Rwork0.1762 --
obs0.1789 50535 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.209 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4166 Å20 Å22.1752 Å2
2--12.9441 Å20 Å2
3----6.5275 Å2
Refinement stepCycle: LAST / Resolution: 2.45→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 3072 11 301 7754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078038
X-RAY DIFFRACTIONf_angle_d1.23911498
X-RAY DIFFRACTIONf_dihedral_angle_d24.0033224
X-RAY DIFFRACTIONf_chiral_restr0.0611293
X-RAY DIFFRACTIONf_plane_restr0.003923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.53760.33352800.2564713X-RAY DIFFRACTION99
2.5376-2.63910.31492220.2334782X-RAY DIFFRACTION99
2.6391-2.75920.30372470.21974790X-RAY DIFFRACTION99
2.7592-2.90470.26192650.19544779X-RAY DIFFRACTION99
2.9047-3.08660.2452540.17594750X-RAY DIFFRACTION99
3.0866-3.32490.21752730.15714802X-RAY DIFFRACTION99
3.3249-3.65930.21662650.14974816X-RAY DIFFRACTION99
3.6593-4.18840.20822480.14954820X-RAY DIFFRACTION99
4.1884-5.27540.16832510.13384883X-RAY DIFFRACTION100
5.2754-42.65660.19832590.1614836X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5829-2.3801-0.60012.42981.1261.5173-0.3068-0.39730.0845-0.17120.2607-0.20670.00180.14860.01940.32820.0349-0.00290.1934-0.01590.2398-19.61354.6593-25.257
26.53731.10920.23210.80761.05092.0603-0.074-0.92561.34770.06220.1785-0.2261-0.4817-0.2377-0.02790.34220.07560.04130.1636-0.10440.4067-20.446913.628-22.4614
36.0311-1.5854-0.70392.10380.77911.37990.24490.32620.2832-0.565-0.1282-0.355-0.22290.0422-0.13250.35320.03030.10960.05390.03320.2465-7.9854.4156-37.4084
44.4723-0.75580.78142.5187-0.45934.4074-0.5451-1.0908-0.247-0.37470.5681-0.83040.50170.7115-0.12660.29850.01570.18380.55610.03440.56428.7257-2.0656-31.8538
51.0001-1.45410.40972.1839-1.19023.2785-1.0248-1.6454-0.64670.07290.73980.17030.36750.340.18380.13990.06470.11480.42280.0840.4567-28.3185-1.2553-14.5867
64.2245-1.1479-1.06821.66310.43450.2776-0.9417-1.1125-0.41510.3360.28560.12740.4690.07070.510.31230.16720.13260.55690.13330.3595-22.2598-2.7473-16.8219
78.2279-1.5755-3.56021.18820.55942.9142-0.083-1.1040.7597-0.44920.4235-0.6549-0.11171.1251-0.40750.4297-0.08150.3170.57260.05690.735913.4231-2.3177-36.6782
80.9448-0.36040.48312.24081.0652.49070.0769-0.16210.08690.05660.0941-0.1043-0.2271-0.2694-0.1230.3260.01220.05840.12640.08960.2921-0.944642.1457-42.269
91.3534-1.30471.22871.6718-1.14394.50790.1025-0.0018-0.1028-0.1938-0.0504-0.79930.29981.0918-0.05350.2496-0.0050.05530.29580.00670.355120.342238.3956-36.9418
102.45220.6343-1.34970.37440.21692.20090.044-1.4409-0.85450.24650.3747-0.44070.00330.3771-0.35570.33780.0199-0.12290.66690.10840.467920.120230.541-21.7162
110.46060.0428-0.17271.3546-1.16664.0832-0.0936-0.6465-0.6068-0.07310.46440.2584-0.0321-1.1464-0.27280.3322-0.0353-0.1560.41910.0820.2608-13.493333.2507-44.9117
120.75860.01150.53152.38470.86682.1205-0.1464-0.1584-0.76750.32810.08330.1958-0.1086-0.76370.16070.3315-0.0292-0.01190.37620.1140.3317-8.306931.5576-40.7144
134.32141.6712-1.96833.6382-0.1271.1032-0.3052-1.615-0.15440.33520.6426-1.14-0.57241.2227-0.22950.4351-0.0161-0.25531.139-0.11690.620726.639230.3127-20.174
140.6303-1.4243-0.69923.19571.37361.50630.1516-0.16540.0387-0.04130.0621-0.0172-0.28720.1385-0.21130.2978-0.02460.01650.1606-0.01840.2953-49.178245.08538.1328
151.3423-0.89590.451.60611.20422.3106-0.008-0.08060.1264-0.1294-0.04620.0705-0.27480.08240.05160.32820.00060.00990.16350.0070.2565-52.046142.57891.7221
163.52-0.5664-0.14571.64790.48521.0835-0.16170.5003-0.2987-0.65070.16710.13610.1863-0.2996-0.06510.30550.0281-0.00830.1270.05090.1793-53.626736.3818-14.3453
174.85980.6605-0.36372.93241.31190.8683-0.060.8784-0.0068-0.92170.5471-0.31370.04330.4205-0.33410.454-0.0810.16230.3618-0.01010.1569-39.956934.0535-19.1881
181.8133-1.1932-1.0851.05451.68424.02110.132-0.590.00490.12590.49950.21940.49271.1097-0.45060.45180.08080.11650.5143-0.03110.216-43.143536.155321.6893
191.1836-1.2287-1.70892.49763.32875.74140.3788-0.49480.19740.31520.5599-0.18570.53680.611-0.6910.30880.0853-0.0040.5152-0.02890.2649-41.940234.681315.067
205.63631.2205-1.47852.7765-0.59720.4581-0.20731.4001-0.5532-0.95630.7207-0.1522-0.61190.7655-0.20360.7447-0.11940.08010.64860.00650.2583-42.000933.3245-25.923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:48)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 49:75)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 76:183)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:14)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 15:25)
6X-RAY DIFFRACTION6(CHAIN D AND RESID 1:15)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 16:25)
8X-RAY DIFFRACTION8(CHAIN E AND RESID 5:95)
9X-RAY DIFFRACTION9(CHAIN E AND RESID 96:180)
10X-RAY DIFFRACTION10(CHAIN F AND RESID 1:14)
11X-RAY DIFFRACTION11(CHAIN G AND RESID 15:25)
12X-RAY DIFFRACTION12(CHAIN H AND RESID 1:15)
13X-RAY DIFFRACTION13(CHAIN H AND RESID 16:25)
14X-RAY DIFFRACTION14(CHAIN I AND RESID 5:65)
15X-RAY DIFFRACTION15(CHAIN I AND RESID 66:125)
16X-RAY DIFFRACTION16(CHAIN I AND RESID 126:179)
17X-RAY DIFFRACTION17(CHAIN J AND RESID 1:14)
18X-RAY DIFFRACTION18(CHAIN K AND RESID 15:25)
19X-RAY DIFFRACTION19(CHAIN L AND RESID 1:15)
20X-RAY DIFFRACTION20(CHAIN L AND RESID 16:25)

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