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- PDB-2v0s: crystal structure of a hairpin exchange variant (LR1) of the targ... -

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Basic information

Entry
Database: PDB / ID: 2v0s
Titlecrystal structure of a hairpin exchange variant (LR1) of the targeting LINE-1 retrotransposon endonuclease
ComponentsLR1
KeywordsTRANSCRIPTION / APE-1 TYPE / ENDONUCLEASE / RETROTRANSPOSITION / RETROTRANSPOSON / PROTEIN ENGINEERING / HYPOTHETICAL PROTEIN
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 / catalytic activity / RNA-directed DNA polymerase activity / RNA-directed DNA polymerase / 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
: / LINE-1 retrotransposable element ORF2 protein / RNA-directed DNA polymerase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRepanas, K. / Zingler, N. / Layer, L.E. / Schumann, G.G. / Perrakis, A. / Weichenrieder, O.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Determinants for DNA Target Structure Selectivity of the Human Line-1 Retrotransposon Endonuclease.
Authors: Repanas, K. / Zingler, N. / Layer, L.E. / Schumann, G.G. / Perrakis, A. / Weichenrieder, O.
History
DepositionMay 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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
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_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1075
Polymers26,7681
Non-polymers3394
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.698, 67.648, 128.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

21A-2146-

HOH

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Components

#1: Protein LR1


Mass: 26767.752 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-193,202-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8TE30, UniProt: O00370*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 178 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE IS A VARIANT OF THE PDB ENTRY 1VYB: L1 ENDONUCLEASE DOMAIN. THE LOOP REGION 193-201 ...THIS STRUCTURE IS A VARIANT OF THE PDB ENTRY 1VYB: L1 ENDONUCLEASE DOMAIN. THE LOOP REGION 193-201 IS REPLACED WITH A LOOP BELONGING TO RELATED ENDONUCLEASE.

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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: 2.25 Å3/Da / Density % sol: 44.86 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 23062 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.89 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYB

1vyb


Resolution: 1.8→80 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.607 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1190 5.2 %RANDOM
Rwork0.188 ---
obs0.19 21871 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.79 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.8→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 17 178 2022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221875
X-RAY DIFFRACTIONr_bond_other_d0.0010.021304
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9632526
X-RAY DIFFRACTIONr_angle_other_deg1.01333198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.424.07481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07815368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5031513
X-RAY DIFFRACTIONr_chiral_restr0.1860.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02349
X-RAY DIFFRACTIONr_nbd_refined0.2130.2371
X-RAY DIFFRACTIONr_nbd_other0.20.21322
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2903
X-RAY DIFFRACTIONr_nbtor_other0.0850.2988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0610.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3770.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.351.51502
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48821863
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7113824
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6864.5663
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
Rfree0.35 88
Rwork0.241 1655

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