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- PDB-2v0r: crystal structure of a hairpin exchange variant (LTx) of the targ... -

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Basic information

Entry
Database: PDB / ID: 2v0r
Titlecrystal structure of a hairpin exchange variant (LTx) of the targeting LINE-1 retrotransposon endonuclease
ComponentsLTX
KeywordsTRANSCRIPTION / APE-1 TYPE / ENDONUCLEASE / RETROTRANSPOSITION / RETROTRANSPOSON / PROTEIN ENGINEERING
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 / telomerase 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
LINE-1 retrotransposable element ORF2 protein / RNA-directed DNA polymerase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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

Downloads & links

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Assembly

Deposited unit
A: LTX
B: LTX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2998
Polymers54,7232
Non-polymers5766
Water2,792155
1
A: LTX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7465
Polymers27,3621
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LTX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5543
Polymers27,3621
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.726, 70.142, 130.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LTX


Mass: 27361.500 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-192,202-238
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.26 Å3/Da / Density % sol: 45.06 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 22873 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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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: 2.3→19.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.859 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1156 5.1 %RANDOM
Rwork0.214 ---
obs0.217 21588 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 30 155 3944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223852
X-RAY DIFFRACTIONr_bond_other_d0.0020.022673
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9655197
X-RAY DIFFRACTIONr_angle_other_deg1.13536545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1745469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0823.69168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62415756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8151530
X-RAY DIFFRACTIONr_chiral_restr0.1130.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024132
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02726
X-RAY DIFFRACTIONr_nbd_refined0.2210.2757
X-RAY DIFFRACTIONr_nbd_other0.2120.22796
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21780
X-RAY DIFFRACTIONr_nbtor_other0.0930.22192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4781.53033
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66523810
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18731687
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2024.51386
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 79
Rwork0.256 1502
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.38930.0518-0.57161.4229-0.68034.37410.0935-0.14450.04610.1839-0.1114-0.09540.05730.21210.0179-0.1742-0.0067-0.0355-0.1382-0.004-0.048921.989426.985815.003
21.4991-0.05591.51791.0285-0.74577.4136-0.03730.2678-0.0059-0.0248-0.0712-0.0858-0.74860.43990.1084-0.1078-0.02750.0131-0.1220.0067-0.033921.07343.4609-15.1114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 230
2X-RAY DIFFRACTION2B20 - 230

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