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- PDB-3mx9: Molecular basis of engineered meganuclease targeting of the endog... -

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Basic information

Entry
Database: PDB / ID: 3mx9
TitleMolecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus
Components
  • DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
  • Protein scV3V2(G19S)
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA complex
Function / homologyHoming endonucleases / Endonuclease I-creI / Roll / Alpha Beta / DNA / DNA (> 10)
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMunoz, I.G. / Prieto, J. / Subramanian, S. / Coloma, J. / Montoya, G.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus.
Authors: Munoz, I.G. / Prieto, J. / Subramanian, S. / Coloma, J. / Redondo, P. / Villate, M. / Merino, N. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Grizot, S. / Daboussi, F. / Smith, J. / ...Authors: Munoz, I.G. / Prieto, J. / Subramanian, S. / Coloma, J. / Redondo, P. / Villate, M. / Merino, N. / Marenchino, M. / D'Abramo, M. / Gervasio, F.L. / Grizot, S. / Daboussi, F. / Smith, J. / Chion-Sotinel, I. / Paques, F. / Duchateau, P. / Alibes, A. / Stricher, F. / Serrano, L. / Blanco, F.J. / Montoya, G.
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: Protein scV3V2(G19S)
C: DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
D: DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7885
Polymers55,7083
Non-polymers802
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-84 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.170, 170.190, 46.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein scV3V2(G19S)


Mass: 40968.719 Da / Num. of mol.: 1 / Mutation: G19S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
#2: DNA chain DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')


Mass: 7320.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')


Mass: 7418.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG 400, 0.1M MES pH 6.5, 5% ethanol, 10% ethylene glycol, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2009 / Details: Bent cylindrical mirror
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→66.33 Å / Num. all: 26888 / Num. obs: 26884 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.3
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3857 / Rsym value: 0.059 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.286 Å / SU ML: 0.36 / σ(F): 2.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 926 5 %RANDOM
Rwork0.1809 ---
obs0.1843 18505 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.964 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.622 Å20 Å20 Å2
2--4.1826 Å2-0 Å2
3----0.5607 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 978 2 58 3374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073477
X-RAY DIFFRACTIONf_angle_d1.2244924
X-RAY DIFFRACTIONf_dihedral_angle_d22.1731319
X-RAY DIFFRACTIONf_chiral_restr0.063569
X-RAY DIFFRACTIONf_plane_restr0.004462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.73720.34771280.23742435X-RAY DIFFRACTION100
2.7372-2.90870.30351300.21732468X-RAY DIFFRACTION100
2.9087-3.13320.29511310.20282504X-RAY DIFFRACTION100
3.1332-3.44840.24071310.1682480X-RAY DIFFRACTION100
3.4484-3.94710.21621320.16082506X-RAY DIFFRACTION100
3.9471-4.9720.20571320.14012518X-RAY DIFFRACTION100
4.972-45.29310.2481420.19562668X-RAY DIFFRACTION99
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)
11.7282-0.5914-0.80690.70280.67651.87810.00350.0131-0.0474-0.08370.0528-0.09890.04590.0862-0.03320.27820.021-0.05140.0716-0.0490.128138.0374-27.565-20.8049
20.8301-0.3388-0.17241.26190.30841.3821-0.005-0.12370.13420.3994-0.0352-0.0896-0.6425-0.50690.00250.33150.1398-0.00590.2615-0.03490.045116.4867-13.8256-5.5221
30.7821-0.2745-0.69961.0520.91861.10560.0112-0.20260.0330.0683-0.1462-0.016-0.2489-0.61390.13510.28910.1275-0.09740.4398-0.0130.07138.831-18.1286-8.4978
40.45370.64820.61710.9610.92640.92430.62640.64810.0414-0.0424-0.264-0.10020.067-0.026-0.29020.2143-0.12250.24570.8732-0.34840.7495-5.1025-24.01997.6114
54.6473-0.21471.93790.2757-0.58581.91980.01470.084-0.43870.13830.12040.1263-0.8627-1.0166-0.03330.36650.4656-0.06560.6979-0.18410.190912.166-8.5662.0641
61.08070.1038-0.29370.1584-0.00410.0893-0.1903-0.0576-0.14930.02440.1616-0.1750.42690.02730.02870.32480.0650.04490.25110.04990.155926.4171-27.851-1.525
70.27830.1058-0.08550.1220.13260.6441-0.02030.1311-0.15260.1508-0.00650.16690.18540.238-0.00070.35130.20260.0940.306-0.18380.320245.5382-41.733-15.466
82.3727-0.48720.9980.7928-0.61090.6635-0.17390.0264-0.52480.16710.0251-0.19520.2142-0.0908-0.00020.37650.22640.07680.4006-0.09920.229742.361-39.3807-13.9049
92.0923-1.2963-1.04990.80040.72791.0855-0.4476-0.5730.17980.15890.4960.10570.04340.2418-0.02130.25330.1778-0.04370.2727-0.01750.18121.9772-20.61-0.3474
101.5218-0.36760.78940.4331-0.17150.41150.44210.91680.2892-0.1347-0.51840.0907-0.9476-0.7984-0.14420.69020.7439-0.06430.8183-0.08510.22949.5939-2.56336.2889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:208)
2X-RAY DIFFRACTION2(chain A and resid 209:252)
3X-RAY DIFFRACTION3(chain A and resid 253:338)
4X-RAY DIFFRACTION4(chain A and resid 339:344)
5X-RAY DIFFRACTION5(chain C and resid 501:509)
6X-RAY DIFFRACTION6(chain C and resid 510:515)
7X-RAY DIFFRACTION7(chain C and resid 516:524)
8X-RAY DIFFRACTION8(chain D and resid 601:611)
9X-RAY DIFFRACTION9(chain D and resid 612:619)
10X-RAY DIFFRACTION10(chain D and resid 620:624)

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