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- PDB-1vyb: Endonuclease domain of human LINE1 ORF2p -

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Basic information

Entry
Database: PDB / ID: 1vyb
TitleEndonuclease domain of human LINE1 ORF2p
ComponentsORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN
KeywordsTRANSFERASE / ENDONUCLEASE / APE-1 TYPE / RETROTRANSPOSITION / RETROTRANSPOSON / RNA-DIRECTED DNA POLYMERASE
Function / homology
Function and homology information


nucleic acid metabolic process / retrotransposition / type II site-specific deoxyribonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / DNA recombination / RNA binding / metal ion binding
Similarity search - Function
Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 4-Layer Sandwich / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
SULFITE ION / LINE-1 retrotransposable element ORF2 protein / :
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeichenrieder, O. / Repanas, K. / Perrakis, A.
CitationJournal: Structure / Year: 2004
Title: Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.
Authors: Weichenrieder, O. / Repanas, K. / Perrakis, A.
History
DepositionApr 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN
B: ORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,22712
Polymers54,3022
Non-polymers92510
Water8,071448
1
A: ORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6126
Polymers27,1511
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6166
Polymers27,1511
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.044, 126.477, 43.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2123-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.39, 0.028, -0.92), (-0.024, -0.999, -0.04), (-0.92, 0.038, -0.389)
Vector: 1.21795, 406.41736, 2.42721)

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Components

#1: Protein ORF2 CONTAINS A REVERSE TRANSCRIPTASE DOMAIN / LINE-1 REVERSE TRANSCRIPTASE HOMOLOG


Mass: 27151.244 Da / Num. of mol.: 2 / Fragment: ENDONUCLEASE DOMAIN, RESIDUES 1-238
Source method: isolated from a genetically manipulated source
Details: NOT OFFICIALLY ASSIGNED TO EC 4.2.99.18, BUT THAT IS THE CLOSEST GROUP
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15-L1EN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15606, UniProt: O00370*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.28 Å3/Da / Density % sol: 45 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 685558 / % possible obs: 97.5 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.4 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DEW

1dew


Resolution: 1.8→20.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.047 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2329 5.1 %RANDOM
Rwork0.186 ---
obs0.188 43461 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.08 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å20 Å20 Å2
2---2.37 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 49 448 4261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213871
X-RAY DIFFRACTIONr_bond_other_d0.0010.023525
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9535223
X-RAY DIFFRACTIONr_angle_other_deg0.87238249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50923.772167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07415742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.221526
X-RAY DIFFRACTIONr_chiral_restr0.1050.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02731
X-RAY DIFFRACTIONr_nbd_refined0.2110.2717
X-RAY DIFFRACTIONr_nbd_other0.1860.23560
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4261.53067
X-RAY DIFFRACTIONr_mcbond_other0.3111947
X-RAY DIFFRACTIONr_mcangle_it1.57223811
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.81531725
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.914.51412
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 141
Rwork0.249 2803

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