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- PDB-2yha: Crystal Structure of the N. crassa QDE-2 AGO MID-PIWI Domains -

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Basic information

Entry
Database: PDB / ID: 2yha
TitleCrystal Structure of the N. crassa QDE-2 AGO MID-PIWI Domains
ComponentsPOST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2RNA interference
KeywordsRNA BINDING PROTEIN / ARGONAUTE / MIRNA / SIRNA
Function / homology
Function and homology information


RNA endonuclease activity / single-stranded RNA binding
Similarity search - Function
Argonaute-like, PIWI domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. ...Argonaute-like, PIWI domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Post-transcriptional gene silencing protein QDE-2
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBoland, A. / Weichenrieder, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal Structure of the Mid-Piwi Lobe of a Eukaryotic Argonaute Protein
Authors: Boland, A. / Huntzinger, E. / Schmidt, S. / Izaurralde, E. / Weichenriede, O.
History
DepositionApr 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: POST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1753
Polymers42,9861
Non-polymers1882
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.080, 63.080, 170.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein POST-TRANSCRIPTIONAL GENE SILENCING PROTEIN QDE-2 / RNA interference


Mass: 42986.453 Da / Num. of mol.: 1 / Fragment: MID-PIWI DOMAINS, RESIDUES 506-786 AND 839-938
Source method: isolated from a genetically manipulated source
Details: RESIDUES 787-838 REPLACED BY THREE-RESIDUE LINKER / Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9P8T1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 4 AMINO ACIDS (GAMA) ARISE FROM THE CLONING SITE RESIDUES R787 TO R838 OF UNIPROT ENTRY ...THE FIRST 4 AMINO ACIDS (GAMA) ARISE FROM THE CLONING SITE RESIDUES R787 TO R838 OF UNIPROT ENTRY Q9P8T1 WERE REPLACED BY A GSG LINKER (GIVEN RESIDUE NUMBERS 787, 837, AND 838 HERE).

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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: 2.39 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 7.2
Details: 200 MM DI-SODIUM TARTRATE, 2.3 M AMMONIUM SULFATE., pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→54.6 Å / Num. obs: 34431 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.07 % / Biso Wilson estimate: 28.85 Å2 / Rsym value: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 5.07 % / Mean I/σ(I) obs: 2.39 / Rsym value: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YHB

2yhb


Resolution: 1.85→54.629 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 23.84 / Stereochemistry target values: ML
Details: THE FOLLOWING RESIDUES ARE DISORDERED, K786 TO A840, F873 TO I882. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS: H841, Y842, K857, D860, T861, L862, E863, Q864, T866, ...Details: THE FOLLOWING RESIDUES ARE DISORDERED, K786 TO A840, F873 TO I882. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS: H841, Y842, K857, D860, T861, L862, E863, Q864, T866, H867, Y871, L872. HYDROGENS WERE REFINED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2363 1087 3.2 %
Rwork0.1959 --
obs0.1972 34415 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.199 Å2 / ksol: 0.422 e/Å3
Displacement parametersBiso mean: 36.76 Å2
Baniso -1Baniso -2Baniso -3
1-5.299 Å20 Å20 Å2
2--5.299 Å20 Å2
3----10.5981 Å2
Refinement stepCycle: LAST / Resolution: 1.85→54.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 11 213 3065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152914
X-RAY DIFFRACTIONf_angle_d1.4533952
X-RAY DIFFRACTIONf_dihedral_angle_d14.3531067
X-RAY DIFFRACTIONf_chiral_restr0.093442
X-RAY DIFFRACTIONf_plane_restr0.007510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.93420.3221140.2574093X-RAY DIFFRACTION100
1.9342-2.03620.27271390.22754136X-RAY DIFFRACTION100
2.0362-2.16380.26071280.20494091X-RAY DIFFRACTION100
2.1638-2.33090.25841520.19314125X-RAY DIFFRACTION100
2.3309-2.56540.25871300.18824114X-RAY DIFFRACTION100
2.5654-2.93670.22181460.1914161X-RAY DIFFRACTION100
2.9367-3.69980.23451320.18234222X-RAY DIFFRACTION100
3.6998-54.65270.21571460.19664386X-RAY DIFFRACTION99

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