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- PDB-2w7a: Structure of the human LINE-1 ORF1p central domain -

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Basic information

Entry
Database: PDB / ID: 2w7a
TitleStructure of the human LINE-1 ORF1p central domain
ComponentsLINE-1 ORF1P
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN
Function / homology
Function and homology information


retrotransposition / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / nucleotide binding / nucleolus / identical protein binding / cytoplasm
Similarity search - Function
L1 transposable element, RRM domain / L1 transposable element, trimerization domain / L1 transposable element trimerization domain / Transposase, L1 / L1 transposable element, dsRBD-like domain / L1 transposable element, C-terminal domain / L1 transposable element, RRM domain / L1 transposable element RBD-like domain / L1 transposable element dsRBD-like domain / Alpha-Beta Plaits ...L1 transposable element, RRM domain / L1 transposable element, trimerization domain / L1 transposable element trimerization domain / Transposase, L1 / L1 transposable element, dsRBD-like domain / L1 transposable element, C-terminal domain / L1 transposable element, RRM domain / L1 transposable element RBD-like domain / L1 transposable element dsRBD-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / LINE-1 retrotransposable element ORF1 protein / LINE-1 retrotransposable element ORF1 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsKhazina, E. / Weichenrieder, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Non-Ltr Retrotransposons Encode Noncanonical Rrm Domains in Their First Open Reading Frame.
Authors: Khazina, E. / Weichenrieder, O.
History
DepositionDec 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LINE-1 ORF1P
B: LINE-1 ORF1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3543
Polymers23,2522
Non-polymers1021
Water5,368298
1
A: LINE-1 ORF1P


Theoretical massNumber of molelcules
Total (without water)11,6261
Polymers11,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LINE-1 ORF1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7282
Polymers11,6261
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.360, 54.710, 57.810
Angle α, β, γ (deg.)90.00, 102.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LINE-1 ORF1P / ORF1 CODES FOR A 40 KDA PRODUCT


Mass: 11625.987 Da / Num. of mol.: 2 / Fragment: RRM DOMAIN, RESIDUES 157-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: Q15605, UniProt: Q9UN81*PLUS
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 7 / Details: 2.2 M NA-MALONATE, PH7.0

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97154
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 27, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111)MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97154 Å / Relative weight: 1
ReflectionResolution: 1.4→56 Å / Num. obs: 38608 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.9
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.8 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHARPphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→56.34 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.357 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1916 5 %RANDOM
Rwork0.135 ---
obs0.138 36445 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20.1 Å2
2---0.36 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.4→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 7 298 1909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221743
X-RAY DIFFRACTIONr_bond_other_d0.0020.021285
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9872367
X-RAY DIFFRACTIONr_angle_other_deg0.97633143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5035230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58623.33387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32115369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6241525
X-RAY DIFFRACTIONr_chiral_restr0.1030.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211935
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02338
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.344121053
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.746161739
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.15324690
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.50636612
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: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 113
Rwork0.196 2645

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