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- PDB-7ocz: Crystal Structure of the PID-3 RRM domain -

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Basic information

Entry
Database: PDB / ID: 7ocz
TitleCrystal Structure of the PID-3 RRM domain
ComponentsProtein pid-3
KeywordsRNA BINDING PROTEIN / piRNA biogenesis 21U RNA RNA recognition motif RNA binding
Function / homology
Function and homology information


21U-RNA metabolic process / positive regulation of chromosome segregation / RNA cap binding complex / piRNA processing / embryo development ending in birth or egg hatching / positive regulation of cell division / chromosome segregation / cell division / perinuclear region of cytoplasm / nucleus / cytoplasm
Similarity search - Function
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBasquin, J. / Ketting, R.F. / Falk, S.
CitationJournal: Genes Dev. / Year: 2021
Title: Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans .
Authors: Perez-Borrajero, C. / Podvalnaya, N. / Holleis, K. / Lichtenberger, R. / Karaulanov, E. / Simon, B. / Basquin, J. / Hennig, J. / Ketting, R.F. / Falk, S.
History
DepositionApr 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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: Protein pid-3
B: Protein pid-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3924
Polymers18,3212
Non-polymers712
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-21 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.294, 43.294, 158.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Protein pid-3 / piRNA biogenesis and chromosome segregation protein 1 / piRNA-induced silencing defective protein 3


Mass: 9160.454 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pid-3, pics-1, Y23H5A.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76616
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.03 M Sodium nitrate, 0.03 M Sodium phosphatedibasic 0.03 M Ammonium sulfate 0.1 M HEPES, 0.1 M MOPS pH 7.5 20% v/v PEG 500 MME; 10% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.28 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.82→37.49 Å / Num. obs: 14314 / % possible obs: 95.02 % / Redundancy: 17.9 % / Biso Wilson estimate: 24.56 Å2 / CC1/2: 0.987 / CC star: 0.997 / Net I/σ(I): 38.78
Reflection shellResolution: 1.82→1.885 Å / Mean I/σ(I) obs: 0.56 / Num. unique obs: 1050 / CC1/2: 0.436 / CC star: 0.779

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
xia2data reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OCX

7ocx


Resolution: 1.82→36.48 Å / SU ML: 0.2361 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.6348
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 778 5.46 %
Rwork0.1823 13467 -
obs0.1838 14245 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.77 Å2
Refinement stepCycle: LAST / Resolution: 1.82→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 2 106 1340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051250
X-RAY DIFFRACTIONf_angle_d0.85451691
X-RAY DIFFRACTIONf_chiral_restr0.0543195
X-RAY DIFFRACTIONf_plane_restr0.0045222
X-RAY DIFFRACTIONf_dihedral_angle_d5.425172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.930.3033990.27241767X-RAY DIFFRACTION75.09
1.93-2.080.26241300.19532304X-RAY DIFFRACTION96.86
2.08-2.290.19741210.20772339X-RAY DIFFRACTION98.91
2.29-2.620.20271450.19012318X-RAY DIFFRACTION99.43
2.63-3.310.22911520.18822361X-RAY DIFFRACTION99.76
3.31-37.490.18531310.15832378X-RAY DIFFRACTION99.96

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