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

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Basic information

Entry
Database: PDB / ID: 2vbj
TitleMolecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers
Components
  • (DNA ENDONUCLEASE I- ...) x 2
  • 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3'
  • 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3'
KeywordsHYDROLASE/DNA / DOUBLE STRAND BREAK (DSB) / CUTTING DNA ENDONUCLEASES / AMEL3-4-CALCIUM / UV-INDUCED DNA DAMAGE / HOMING ENDONUCLEASES (HES) / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / Structure summary / Version format compliance
Revision 1.2May 29, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Dec 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_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: DNA ENDONUCLEASE I-CREI
B: DNA ENDONUCLEASE I-CREI
C: 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3'
E: 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8376
Polymers49,7574
Non-polymers802
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-95.2 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.552, 68.700, 88.731
Angle α, β, γ (deg.)90.00, 95.36, 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 / AMEL3-4-CA / 23S RRNA INTRON PROTEIN


Mass: 17566.201 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Description: AMEL4 STREP-TAG C-TERM AMEL3 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 / AMEL3-4-CA / 23S RRNA INTRON PROTEIN


Mass: 17454.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Description: AMEL4 STREP-TAG C-TERM AMEL3 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 , 2 types, 2 molecules CE

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


Mass: 7325.738 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3'


Mass: 7410.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 332 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.56 Å3/Da / Density % sol: 59.13 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING-DROP DNA-PROTEIN COMPLEX SOLUTION WAS 4 MG/ML. 35% 2-ETHOXYETHANOL IN 0.1M NA-CACODYLATE PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.983
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.95→32.88 Å / Num. obs: 35740 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.95→2.001 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / % possible all: 96.7

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Processing

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

1g9z


Resolution: 1.95→32.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.01 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1949 5.2 %RANDOM
Rwork0.147 ---
obs0.15 35736 96.7 %-
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: 42.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.1 Å2
2--0.34 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 978 2 330 3766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223596
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0812.3135065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6865302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.74624.821112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87815477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2571513
X-RAY DIFFRACTIONr_chiral_restr0.1430.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022335
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21500
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22331
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2317
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.10.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3250.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9941.51565
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.24422466
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.19832638
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.6954.52599
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 115 -
Rwork0.141 2087 -
obs--77.59 %

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