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- PDB-2vbn: Molecular basis of human XPC gene recognition and cleavage by eng... -

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Basic information

Entry
Database: PDB / ID: 2vbn
TitleMolecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers
Components
  • (DNA ENDONUCLEASE I- ...) x 2
  • 5'-D(*AP*AP*AP*AP*GP*GP*CP*AP*GP*AP)-3'
  • 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*AP*AP)-3'
  • 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP)-3'
  • 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP)-3'
KeywordsHYDROLASE / UV-INDUCED DNA DAMAGE / CUTTING DNA ENDONUCLEASES / ENDONUCLEASE / INTRON HOMING / INI3- 4_MAGNESIUM / PLASTID / NUCLEASE / CHLOROPLAST / DOUBLE STRAND BREAK (DSB) / HOMING ENDONUCLEASES (HES)
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / identical protein binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRedondo, P. / Prieto, J. / Munoz, I.G. / Alibes, A. / Stricher, F. / Serrano, L. / Arnould, S. / Perez, C. / Cabaniols, J.P. / Duchateau, P. ...Redondo, P. / Prieto, J. / Munoz, I.G. / Alibes, A. / Stricher, F. / Serrano, L. / Arnould, S. / Perez, C. / Cabaniols, J.P. / Duchateau, P. / Paques, F. / Blanco, F.J. / Montoya, G.
CitationJournal: Nature / Year: 2008
Title: Molecular Basis of Xeroderma Pigmentosum Group C DNA Recognition by Engineered Meganucleases
Authors: Redondo, P. / Prieto, J. / Munoz, I.G. / Alibes, A. / Stricher, F. / Serrano, L. / Cabaniols, J.P. / Daboussi, F. / Arnould, S. / Perez, C. / Duchateau, P. / Paques, F. / Blanco, F.J. / Montoya, G.
History
DepositionSep 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: 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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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: DNA ENDONUCLEASE I-CREI
B: DNA ENDONUCLEASE I-CREI
C: 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP)-3'
E: 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP)-3'
S: 5'-D(*AP*AP*AP*AP*GP*GP*CP*AP*GP*AP)-3'
T: 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*AP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,90711
Polymers49,7546
Non-polymers1535
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-114.4 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.115, 67.992, 77.186
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA ENDONUCLEASE I- ... , 2 types, 2 molecules AB

#1: Protein DNA ENDONUCLEASE I-CREI / 23S RRNA INTRON PROTEIN / INI3-4-MG


Mass: 17529.184 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Description: INI3 STREP-TAG C-TERM INI4 HIS-TAG C-TERM / Plasmid: CDFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / Variant (production host): D3PLYSS
References: UniProt: P05725, Hydrolases; Acting on ester bonds
#2: Protein DNA ENDONUCLEASE I-CREI / 23S RRNA INTRON PROTEIN / INI3-4-MG


Mass: 17578.250 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Description: INI3 STREP-TAG C-TERM INI4 HIS-TAG C-TERM / Plasmid: CDFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / Variant (production host): D3PLYSS
References: UniProt: P05725, Hydrolases; Acting on ester bonds

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DNA chain , 4 types, 4 molecules CEST

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


Mass: 4254.791 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP)-3'


Mass: 4227.749 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain 5'-D(*AP*AP*AP*AP*GP*GP*CP*AP*GP*AP)-3'


Mass: 3111.082 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: DNA chain 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*AP*AP)-3'


Mass: 3053.031 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 353 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.27 Å3/Da / Density % sol: 45.37 % / Description: NONE
Crystal growpH: 4.5
Details: 4 MG/ML PROTEIN, 20% PEG1000, 0.1M IMIDAZOLE PH 8.0, 0.2 M CAAC2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.872
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 1.9→46.13 Å / Num. obs: 33531 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9Z

1g9z


Resolution: 1.9→46.13 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.777 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1761 5 %RANDOM
Rwork0.141 ---
obs0.145 33531 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.15 Å2
2--0.07 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 979 5 348 3793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0592.3115069
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5915303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32925.089112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88415477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6951511
X-RAY DIFFRACTIONr_chiral_restr0.140.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022339
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.21607
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22338
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3670.2375
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2090.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3440.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2671.51523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.65122476
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.62832306
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.0474.52593
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 106 -
Rwork0.136 1922 -
obs--73.19 %

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