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- PDB-5a0w: THE CRYSTAL STRUCTURE OF I-DMOI E117A IN COMPLEX WITH ITS TARGET ... -

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Basic information

Entry
Database: PDB / ID: 5a0w
TitleTHE CRYSTAL STRUCTURE OF I-DMOI E117A IN COMPLEX WITH ITS TARGET DNA AND IN THE PRESENCE OF 2MM MN
Components
  • (25MER) x 2
  • HOMING ENDONUCLEASE I-DMOI
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / 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: 2.2 Å
AuthorsMolina, R. / Besker, N. / Prieto, J. / Montoya, G. / D'Abramo, M.
CitationJournal: To be Published
Title: Structural and Dynamical Characterization of the I- Dmo Catalytic Activity
Authors: Molina, R. / Besker, N. / Prieto, J. / Montoya, G. / D'Abramo, M.
History
DepositionApr 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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.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_asym_id / _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)116,58327
Polymers115,7109
Non-polymers87318
Water6,828379
1
D: HOMING ENDONUCLEASE I-DMOI
E: 25MER
F: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8108
Polymers38,5703
Non-polymers2405
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-80.3 kcal/mol
Surface area14230 Å2
MethodPISA
2
A: HOMING ENDONUCLEASE I-DMOI
B: 25MER
C: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,92810
Polymers38,5703
Non-polymers3587
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-72.8 kcal/mol
Surface area14190 Å2
MethodPISA
3
G: HOMING ENDONUCLEASE I-DMOI
H: 25MER
I: 25MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8459
Polymers38,5703
Non-polymers2756
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-77.4 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.928, 69.770, 106.985
Angle α, β, γ (deg.)90.00, 120.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ADG

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


Mass: 23207.021 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFUROCOCCUS MOBILIS (archaea) / Plasmid: PET24D / 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 , 4 types, 397 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.97 Å3/Da / Density % sol: 63 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.89
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.2→29.22 Å / Num. obs: 120214 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 40.72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.8 / % possible all: 95.1

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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: 2.2→29.22 Å / SU ML: 0.34 / σ(F): 0.79 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 6016 5 %
Rwork0.1706 --
obs0.1725 120107 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.13 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1478 Å20 Å2-0.0974 Å2
2--10.9474 Å20 Å2
3----7.7996 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 3057 33 379 8001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078156
X-RAY DIFFRACTIONf_angle_d1.23711652
X-RAY DIFFRACTIONf_dihedral_angle_d23.9583271
X-RAY DIFFRACTIONf_chiral_restr0.0611309
X-RAY DIFFRACTIONf_plane_restr0.004946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.31016060.268810598X-RAY DIFFRACTION82
2.2786-2.36980.26416280.219411222X-RAY DIFFRACTION87
2.3698-2.47760.25435630.203411083X-RAY DIFFRACTION86
2.4776-2.60820.24895600.195611173X-RAY DIFFRACTION86
2.6082-2.77140.24185370.189211188X-RAY DIFFRACTION87
2.7714-2.98520.22716420.173311522X-RAY DIFFRACTION90
2.9852-3.28530.17525810.147611603X-RAY DIFFRACTION90
3.2853-3.75980.1836900.140211765X-RAY DIFFRACTION92
3.7598-4.73370.15836140.126611838X-RAY DIFFRACTION92
4.7337-29.2230.19235950.156512099X-RAY DIFFRACTION93
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)
10.63050.3428-0.22291.5457-1.30511.10890.00370.07270.22550.0905-0.0002-0.05560.1181-0.04370.01350.157-0.0233-0.00250.08550.00860.17537.1622-0.358940.6512
20.58270.51740.29981.5544-0.21322.6648-0.02270.03780.063-0.07690.1270.043-0.2946-0.302-0.08720.1630.06240.00570.13190.05680.15532.66576.216541.3551
30.41150.3122-0.76980.2405-0.52982.1018-0.0734-0.087-0.08740.1494-0.1603-0.1338-0.03130.1940.19450.2451-0.0163-0.00860.16090.00390.244211.77570.475760.1029
41.2275-0.7398-0.31110.59560.34251.4506-0.046-0.2354-0.0056-0.37340.0572-0.0278-0.10280.0451-0.01540.3818-0.0310.01710.0671-0.02720.18196.96122.13764.3027
53.41771.53162.73742.47121.7053.4028-0.0661-0.6327-0.14-0.06180.27050.0391-0.3704-0.8299-0.21250.4538-0.06010.00380.3070.02350.1715-1.4456-6.0275.8778
61.11930.1115-0.09640.97-1.20895.87270.06570.22040.1223-0.26850.41160.1270.998-1.2796-0.36690.3372-0.18040.00190.3650.03690.2163-2.9842-5.051636.2043
71.71930.4197-0.63913.2646-1.875.19590.27060.32370.1251-0.0820.3630.34940.7074-0.8998-0.46190.2513-0.1264-0.04870.2710.06020.1014-1.9663-6.314335.3778
82.2639-0.10012.41621.03-1.0033.45590.0139-0.87980.06780.35660.341-0.1753-0.3332-1.0154-0.26650.3653-0.00340.0410.5304-0.04730.2108-1.9544-6.070776.7028
90.62150.0688-0.1791.07740.89870.8422-0.08740.00660.11-0.10360.0784-0.0326-0.2452-0.03340.14990.14840.08560.00620.01330.05420.200341.2829-0.680623.8322
101.9506-0.2224-0.25440.80210.34621.3617-0.0486-0.23650.312-0.0601-0.03310.0298-0.2603-0.08080.07040.22760.0499-0.00370.0776-0.01580.218844.19285.400527.603
112.37180.40840.05670.4420.14980.2259-0.18050.3159-0.0822-0.32480.06-0.1079-0.1650.14840.06790.3096-0.00260.06350.2496-0.00240.263555.56440.38710.1957
121.85411.12030.18871.6648-0.38951.5435-0.09440.3344-0.0003-0.03110.1421-0.4471-0.30210.3317-0.03720.3069-0.02120.06490.33190.00060.375562.51163.720513.22
130.8575-0.53791.28631.17690.49983.9535-0.4562-0.6343-0.0686-0.0350.3979-0.1220.2461.6872-0.06610.25520.11060.18190.74530.06070.481872.7776-7.947617.366
140.6030.5448-0.43881.7665-0.57930.8531-0.5485-0.5326-0.40470.09920.16870.02390.16420.01690.31120.13830.09030.04290.20160.06640.258636.1508-5.646335.3148
151.57440.8026-0.2722.6791-0.81880.8121-0.4069-0.29650.12360.0824-0.1184-0.3490.3455-0.02190.45330.22850.1270.11160.26750.05060.286240.8902-7.352934.0163
163.1451-1.07420.28041.13990.71621.3752-0.682-0.77690.1157-0.17620.5672-0.13220.4541.724-0.0220.35650.06690.22650.87940.09070.585776.267-7.683912.8828
170.86550.71930.74691.04760.73810.67430.01760.19710.12290.0129-0.0188-0.0097-0.07370.15270.00620.24080.0065-0.00240.1569-0.03290.21779.33020.91012.6198
180.90870.06130.81150.32670.31633.7265-0.43690.04810.3645-0.01450.04990.1089-0.82070.49030.33810.3665-0.0973-0.07030.21090.05670.272510.138612.0492-1.3318
191.37040.94521.36151.77791.44391.5779-0.03070.07730.05380.00120.01670.1384-0.15440.21860.00430.19780.01390.00890.18170.0080.21331.64953.42320.1294
200.7760.07711.26811.1639-0.09582.7043-0.1669-0.22230.12540.19330.07460.26140.0995-0.30.07480.18120.0386-0.05110.15480.00370.2973-12.3502-1.1331-7.4893
211.41720.4319-0.66450.16020.03132.1188-0.37440.89510.0375-0.17470.39680.1628-0.12280.168-0.02440.2791-0.0282-0.13530.4248-0.02970.2905-10.1149-4.8258-21.3043
223.97730.12954.27321.00360.45776.45610.19080.8813-0.86130.0310.3725-0.2086-0.24121.1082-0.42950.29730.0682-0.10020.378-0.14830.315823.6718-3.02772.1716
232.71490.43083.59191.27661.16915.36930.0490.7588-0.766-0.32410.3017-0.0664-0.29140.6959-0.35880.23050.0138-0.07440.536-0.16010.301718.8159-4.3626-2.6618
242.5935-1.2259-0.83342.29020.42160.7934-0.46310.7383-0.325-0.11140.36630.5945-0.2737-0.11970.06140.3062-0.0236-0.13640.45560.10440.3708-17.3112-5.2744-22.8964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:40)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 41:94)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 95:151)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 152:186)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:10)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 11:25)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 1:15)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 16:25)
9X-RAY DIFFRACTION9(CHAIN D AND RESID 5:40)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 41:94)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 95:151)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 152:195)
13X-RAY DIFFRACTION13(CHAIN E AND RESID 1:13)
14X-RAY DIFFRACTION14(CHAIN E AND RESID 14:25)
15X-RAY DIFFRACTION15(CHAIN F AND RESID 1:15)
16X-RAY DIFFRACTION16(CHAIN F AND RESID 16:25)
17X-RAY DIFFRACTION17(CHAIN G AND RESID 5:41)
18X-RAY DIFFRACTION18(CHAIN G AND RESID 42:71)
19X-RAY DIFFRACTION19(CHAIN G AND RESID 72:122)
20X-RAY DIFFRACTION20(CHAIN G AND RESID 123:182)
21X-RAY DIFFRACTION21(CHAIN H AND RESID 1:14)
22X-RAY DIFFRACTION22(CHAIN H AND RESID 15:25)
23X-RAY DIFFRACTION23(CHAIN I AND RESID 1:15)
24X-RAY DIFFRACTION24(CHAIN I AND RESID 16:25)

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