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- PDB-7n8k: LINE-1 endonuclease domain complex with Mg -

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Basic information

Entry
Database: PDB / ID: 7n8k
TitleLINE-1 endonuclease domain complex with Mg
ComponentsLINE-1 retrotransposable element ORF2 protein
KeywordsHYDROLASE / endonuclease / non-LTR retrotransposon
Function / homology
Function and homology information


retrotransposition / nucleic acid metabolic process / 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
Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
ACETATE ION / LINE-1 retrotransposable element ORF2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKorolev, S. / Miller, I.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
Authors: Miller, I. / Totrov, M. / Korotchkina, L. / Kazyulkin, D.N. / Gudkov, A.V. / Korolev, S.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LINE-1 retrotransposable element ORF2 protein
B: LINE-1 retrotransposable element ORF2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20114
Polymers54,3022
Non-polymers89812
Water4,612256
1
A: LINE-1 retrotransposable element ORF2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6418
Polymers27,1511
Non-polymers4907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LINE-1 retrotransposable element ORF2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5606
Polymers27,1511
Non-polymers4095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.857, 126.776, 44.854
Angle α, β, γ (deg.)90.000, 98.944, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein LINE-1 retrotransposable element ORF2 protein / ORF2p


Mass: 27151.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: O00370, RNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6 / Details: 0.1M LiSO4; 26% PEG 2000 MME

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Data collection

DiffractionMean temperature: 180 K / Ambient temp details: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 30980 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.32 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.055 / Rrim(I) all: 0.104 / Χ2: 1.4 / Net I/σ(I): 16.3
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 1505 / CC1/2: 0.627 / CC star: 0.878 / Χ2: 1.29 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYB

1vyb


Resolution: 2.01→33.3 Å / SU ML: 0.2061 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 1997 6.45 %
Rwork0.192 28959 -
obs0.1949 30956 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.53 Å2
Refinement stepCycle: LAST / Resolution: 2.01→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 49 256 4045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813845
X-RAY DIFFRACTIONf_angle_d1.09925189
X-RAY DIFFRACTIONf_chiral_restr0.0532595
X-RAY DIFFRACTIONf_plane_restr0.0043648
X-RAY DIFFRACTIONf_dihedral_angle_d3.46372346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.30911420.26671968X-RAY DIFFRACTION94.11
2.06-2.110.24181380.24462045X-RAY DIFFRACTION96.94
2.11-2.180.25751350.22722025X-RAY DIFFRACTION97.3
2.18-2.250.27731390.22392078X-RAY DIFFRACTION97.49
2.25-2.330.25221500.21472025X-RAY DIFFRACTION97.71
2.33-2.420.2821370.20082045X-RAY DIFFRACTION97.94
2.42-2.530.25291400.20282097X-RAY DIFFRACTION98.37
2.53-2.660.26061500.20312083X-RAY DIFFRACTION98.59
2.66-2.830.25061440.20362078X-RAY DIFFRACTION98.89
2.83-3.050.24691390.19372084X-RAY DIFFRACTION99.2
3.05-3.350.23021510.17962089X-RAY DIFFRACTION99.38
3.35-3.840.21291390.17442100X-RAY DIFFRACTION99.82
3.84-4.830.22261450.15882111X-RAY DIFFRACTION99.78
4.83-33.30.20431480.19462131X-RAY DIFFRACTION99.56

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