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

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Basic information

Entry
Database: PDB / ID: 3mxa
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*C)-3')
  • DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
  • DNA (5'-D(P*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
  • scV3V2(G19S)
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA complex
Function / homologyHoming endonucleases / Endonuclease I-creI / Roll / Alpha Beta / ETHANOL / : / DNA / DNA (> 10)
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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.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: scV3V2(G19S)
C: DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*C)-3')
D: DNA (5'-D(P*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')
E: DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*C)-3')
F: DNA (5'-D(P*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,16012
Polymers55,6185
Non-polymers5417
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-72 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.000, 172.390, 46.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: 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

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DNA chain , 4 types, 4 molecules CDEF

#2: DNA chain DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*C)-3')


Mass: 4261.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#3: DNA chain DNA (5'-D(P*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3')


Mass: 3013.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*C)-3')


Mass: 4311.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#5: DNA chain DNA (5'-D(P*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3')


Mass: 3062.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.

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Non-polymers , 4 types, 127 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
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→35.24 Å / Num. all: 27076 / Num. obs: 27057 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rsym value: 0.081 / Net I/σ(I): 13.4
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3874 / Rsym value: 0.049 / % possible all: 99.5

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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: 2.3→28.95 Å / SU ML: 0.29 / σ(F): 1.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1337 5.04 %RANDOM
Rwork0.1741 ---
obs0.1767 26535 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.888 Å2 / ksol: 0.322 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 980 28 120 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073568
X-RAY DIFFRACTIONf_angle_d1.2585021
X-RAY DIFFRACTIONf_dihedral_angle_d21.7851378
X-RAY DIFFRACTIONf_chiral_restr0.065576
X-RAY DIFFRACTIONf_plane_restr0.004467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.25521390.19952450X-RAY DIFFRACTION99
2.3822-2.47750.25781340.18612469X-RAY DIFFRACTION100
2.4775-2.59020.26341260.18662505X-RAY DIFFRACTION100
2.5902-2.72670.24751230.18442472X-RAY DIFFRACTION100
2.7267-2.89730.26791200.19562522X-RAY DIFFRACTION100
2.8973-3.12080.271390.20462497X-RAY DIFFRACTION100
3.1208-3.43440.21481240.17682529X-RAY DIFFRACTION100
3.4344-3.93030.23691260.16642531X-RAY DIFFRACTION100
3.9303-4.94780.16691430.1342551X-RAY DIFFRACTION100
4.9478-28.95220.19571630.15912672X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.95610.48180.57840.93160.58742.4361-0.0052-0.01250.02090.0050.0311-0.09630.1344-0.2321-0.03280.1328-0.05640.06110.1946-0.02680.1086-23.029511.3113-26.8451
21.4557-0.0883-0.32360.3932-0.27460.29620.3703-0.62690.34630.0177-0.23570.08460.6108-0.6485-0.10030.355-0.58660.12250.592-0.16940.239
31.7437-0.2343-0.15540.890.09130.031-0.0346-0.25040.0482-0.28520.2998-0.0928-0.3379-0.0059-0.20790.3367-0.132-0.0070.27540.05150.1166
42.0704-0.1679-0.52710.7145-0.0510.3131-0.4699-0.08870.0629-0.18430.5788-0.4269-0.13970.3203-0.18480.2536-0.1653-0.12690.456-0.16320.2495
50.7848-0.27141.08940.93480.69362.87070.1156-0.33420.0935-0.10110.4683-0.44260.1024-0.385-0.43350.4382-0.1806-0.16030.6647-0.11660.5346
60.48420.1402-0.4670.0666-0.09460.5145-0.32050.1079-0.1177-0.4520.1423-0.0310.06330.49280.13650.2945-0.23970.0490.4915-0.01520.0977
70.2002-0.0410.52010.30990.17631.63320.0779-0.1564-0.0340.0175-0.0341-0.04880.5554-0.9231-0.04940.458-0.44470.03990.5009-0.0250.2506
Refinement TLS groupSelection details: chain F and resid 615:624)

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