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- PDB-5ak9: THE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TAR... -

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Basic information

Entry
Database: PDB / ID: 5ak9
TitleTHE CRYSTAL STRUCTURE OF I-DMOI Q42AK120M IN COMPLEX WITH ITS TARGET DNA 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 / 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: 2.601 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 2, 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: 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
J: HOMING ENDONUCLEASE I-DMOI
K: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
L: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3
N: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,97219
Polymers115,58412
Non-polymers3897
Water4,197233
1
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)38,6386
Polymers38,5284
Non-polymers1102
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-56.1 kcal/mol
Surface area13880 Å2
MethodPISA
2
J: HOMING ENDONUCLEASE I-DMOI
K: 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*AP)-3'
L: 5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*GP)-3
N: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6386
Polymers38,5284
Non-polymers1102
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-53.5 kcal/mol
Surface area13950 Å2
MethodPISA
3
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)38,6977
Polymers38,5284
Non-polymers1693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-52.4 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.530, 70.880, 107.680
Angle α, β, γ (deg.)90.00, 119.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules AEJ

#1: Protein HOMING ENDONUCLEASE I-DMOI


Mass: 23210.021 Da / Num. of mol.: 3
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 , 3 types, 9 molecules BFKCGLDHN

#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 , 3 types, 240 molecules

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


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 0.54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.59→42.95 Å / Num. obs: 81613 / % possible obs: 97.5 % / Observed criterion σ(I): 1.9 / Redundancy: 3.2 % / Biso Wilson estimate: 42.21 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.9 / % possible all: 92

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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: 2.601→42.947 Å / SU ML: 0.34 / σ(F): 0.9 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 4054 5 %
Rwork0.1695 --
obs0.1722 81107 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.648 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5878 Å20 Å2-1.8041 Å2
2--6.3383 Å20 Å2
3----3.7505 Å2
Refinement stepCycle: LAST / Resolution: 2.601→42.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 3060 10 233 7811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078137
X-RAY DIFFRACTIONf_angle_d1.28511628
X-RAY DIFFRACTIONf_dihedral_angle_d23.5663259
X-RAY DIFFRACTIONf_chiral_restr0.0631303
X-RAY DIFFRACTIONf_plane_restr0.004945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6006-2.69350.35713930.28097459X-RAY DIFFRACTION91
2.6935-2.80130.30794050.25537742X-RAY DIFFRACTION97
2.8013-2.92880.28894050.23197790X-RAY DIFFRACTION97
2.9288-3.08320.2814090.20767800X-RAY DIFFRACTION97
3.0832-3.27630.23834030.17227715X-RAY DIFFRACTION96
3.2763-3.52910.20344130.13717746X-RAY DIFFRACTION96
3.5291-3.88410.21274080.14717730X-RAY DIFFRACTION96
3.8841-4.44560.19494090.13097804X-RAY DIFFRACTION96
4.4456-5.59910.18624040.13267632X-RAY DIFFRACTION95
5.5991-42.95250.17134050.15447635X-RAY DIFFRACTION95
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)
11.4477-0.13780.0261.6845-0.04590.3782-0.17750.0104-0.408-0.06540.18750.02360.1120.32920.06470.14550.09980.0191-0.08210.06110.13310.2366-11.518926.0738
22.5887-0.5041-0.43040.6524-0.16240.2955-0.08220.51540.1283-0.498-0.00540.2654-0.091-0.21470.04760.17370.0142-0.0810.08190.01020.1681-5.21-6.99210.2222
31.9281-0.42280.59841.8998-1.73441.61640.65940.0218-0.97421.53060.05130.53140.02830.2757-0.49480.5776-0.0501-0.20170.1304-0.01360.6227-4.6462-21.661413.8082
40.24590.57780.45471.69570.24137.0012-0.5596-0.08970.1294-0.35510.20560.1484-0.4782-1.84240.44530.1792-0.0385-0.18710.5535-0.11920.3627-21.9644012.8206
55.65891.0487-0.82480.3163-0.87275.2295-0.8672-0.69250.61180.39830.46810.0964-0.0729-0.90920.27290.18580.1784-0.01340.3167-0.09060.2945-8.0566-0.274730.3561
60.83810.4305-0.38311.2640.77593.6096-0.5051-0.11280.05330.3680.3585-0.2425-0.24880.80950.03140.18970.0426-0.11040.2462-0.03680.359712.30361.094534.7568
71.47880.85970.19292.80322.27142.0508-0.6262-0.69520.86620.43731.269-0.4278-0.22870.4351-0.47920.17370.1518-0.07990.52690.00820.387929.7632-9.344937.699
85.33370.8874-0.5510.58720.11540.5397-0.11570.20350.02630.6234-0.1505-0.1812-0.62090.15080.20370.20060.081-0.06360.33090.09120.236419.0695-3.961635.8151
92.9557-1.66872.77361.2487-2.19163.7257-0.5187-0.48580.05790.01670.1960.8595-0.5512-0.90810.28410.19160.083-0.03060.2498-0.05280.3898-10.13971.973224.6869
103.64561.7041-5.15761.6582-1.71327.9926-0.25841.5167-0.1602-0.40781.041-0.67820.4538-2.9196-0.52290.51540.0553-0.27711.0385-0.16310.49-27.24441.28035.0685
110.7920.03010.3122.0257-0.3522.81010.1343-0.1732-0.11160.08560.115-0.15710.3805-0.494-0.21270.0771-0.0615-0.03980.12810.11430.17174.578822.386951.8915
120.804-0.35620.75770.85420.50811.45380.017-0.0101-0.1971-0.1644-0.0787-0.1654-0.09470.0755-0.17130.1014-0.0283-0.0108-0.0050.05910.14819.616628.357236.0627
136.0524-0.2055-1.1690.74490.87676.3051-0.4260.2862-1.1492-0.36550.5875-0.19391.1920.1584-0.00950.33490.01440.0305-0.0006-0.05960.28959.749817.304824.8832
141.1683-2.8696-2.50348.69097.51617.01220.250.18710.41620.1446-0.09520.0477-0.1822-1.4805-0.19510.52740.00930.03930.3499-0.01550.1880.959831.095114.2891
155.4052-5.02536.42245.3064-5.52337.8940.2656-1.5406-0.3396-0.09840.59820.774-0.215-1.045-0.52060.13630.2491-0.03540.47710.02690.2011-9.120434.678934.9263
168.1683-0.7-0.90982.08520.27220.22050.1062-0.54860.62080.03490.57950.2159-1.355-0.5728-0.44190.34680.13070.01130.5839-0.01650.1262-2.412135.402758.2275
176.7922-5.47614.34484.8437-4.10539.2833-0.1711-1.4463-0.885-0.16711.18211.0135-0.5417-1.8256-0.69760.4486-0.0673-0.16960.65750.12540.37485.085225.438374.3596
183.198-0.86742.84820.6381-1.62637.64790.3803-0.40.11480.08160.35710.2883-1.0709-1.5908-0.58790.32280.0407-0.06120.68860.18080.24840.851230.605964.6923
191.25510.2972-3.37492.4605-0.04099.8884-0.06710.2108-0.0309-0.16530.5666-0.0008-0.0923-1.2511-0.02530.26870.2613-0.02740.0597-0.0460.1668-4.565336.287339.6808
200.66040.4746-2.02932.9426-1.10046.15640.29490.6698-0.0365-0.33380.2995-0.35890.0277-1.3882-0.35810.42860.058-0.06920.5184-0.06980.2723-1.322633.606913.2577
211.119-0.4103-0.85411.4322-0.58241.223-0.22280.1419-0.25510.15510.08330.14950.1396-0.1710.11580.0893-0.01890.01290.07830.01380.1358-8.7604-14.083394.17
220.62460.3235-0.36041.6045-0.37871.9527-0.0251-0.084-0.08980.02520.0203-0.23220.06360.04310.00450.03710.0115-0.00120.0649-0.00180.14564.7039-8.682389.915
231.47132.9675-0.95356.1381-1.68510.96490.10080.0506-1.3059-0.5528-0.3755-1.2045-0.2121-0.2890.23580.38780.0191-0.06480.258-0.08310.53498.727-21.855387.7121
241.63130.41781.31582.96222.52.6956-0.5530.7357-0.1934-0.40170.4611-0.21820.06040.7347-0.12440.23110.00160.16850.2997-0.06090.353316.2623-2.508671.1807
254.39010.8737-1.77582.65571.95662.9541-0.49350.4860.3108-0.55590.76190.29111.07230.8082-0.1580.3772-0.0772-0.03090.4410.04980.1048-5.6459-4.995674.6292
260.81360.3441.1821.25830.24991.7130.2933-0.21390.58380.0462-0.13030.0989-0.1214-0.5907-0.13020.19070.05430.14790.47780.13990.3702-19.85-2.334889.9769
275.9909-4.5562-2.93936.43361.78941.5301-0.3823-0.08540.64290.3011.74160.0631-0.0919-0.6929-0.85940.3291-0.2110.16750.35530.06450.1748-30.0279-11.3248105.2591
280.96871.1265-1.20452.375-1.43594.5352-0.17370.5450.7994-0.17890.34750.53110.1446-0.3367-0.02450.1542-0.01580.02760.52740.09080.2239-23.5111-6.819196.0842
296.94532.63291.76391.61660.39730.53360.1580.40370.5995-0.3977-0.02420.30620.4759-0.2156-0.16140.1940.0919-0.01240.32810.03720.2506-4.9076-0.752479.0611
306.3604-0.76653.09572.7452-0.76762.3849-1.31941.41650.66080.36360.6389-0.57710.12850.46910.44950.3051-0.07070.07840.5545-0.14080.458420.1542-1.693768.9996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:95)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 96:174)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 175:187)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:10)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 11:14)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 15:21)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 22:25)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 1:10)
9X-RAY DIFFRACTION9(CHAIN D AND RESID 11:20)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 21:25)
11X-RAY DIFFRACTION11(CHAIN E AND RESID 5:75)
12X-RAY DIFFRACTION12(CHAIN E AND RESID 76:167)
13X-RAY DIFFRACTION13(CHAIN E AND RESID 168:180)
14X-RAY DIFFRACTION14(CHAIN F AND RESID 1:8)
15X-RAY DIFFRACTION15(CHAIN F AND RESID 9:14)
16X-RAY DIFFRACTION16(CHAIN G AND RESID 15:21)
17X-RAY DIFFRACTION17(CHAIN G AND RESID 22:25)
18X-RAY DIFFRACTION18(CHAIN H AND RESID 1:10)
19X-RAY DIFFRACTION19(CHAIN H AND RESID 11:17)
20X-RAY DIFFRACTION20(CHAIN H AND RESID 18:25)
21X-RAY DIFFRACTION21(CHAIN J AND RESID 5:64)
22X-RAY DIFFRACTION22(CHAIN J AND RESID 65:174)
23X-RAY DIFFRACTION23(CHAIN J AND RESID 175:187)
24X-RAY DIFFRACTION24(CHAIN K AND RESID 1:10)
25X-RAY DIFFRACTION25(CHAIN K AND RESID 11:14)
26X-RAY DIFFRACTION26(CHAIN L AND RESID 15:21)
27X-RAY DIFFRACTION27(CHAIN L AND RESID 22:25)
28X-RAY DIFFRACTION28(CHAIN N AND RESID 1:10)
29X-RAY DIFFRACTION29(CHAIN N AND RESID 11:17)
30X-RAY DIFFRACTION30(CHAIN N AND RESID 18:25)

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