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

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Basic information

Entry
Database: PDB / ID: 2yhb
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


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 / PAZ domain profile. / 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: 3.65 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 1.1Aug 31, 2011Group: Database references / Version format compliance
Revision 1.2Dec 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)49,0653
Polymers48,8771
Non-polymers1882
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)218.910, 218.910, 76.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 48877.121 Da / Num. of mol.: 1 / Fragment: MID-PIWI DOMAINS, RESIDUES 506-938
Source method: isolated from a genetically manipulated source
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
Sequence detailsTHE FIRST 4 AMINO ACIDS (GAMA) ARISE FROM THE CLONING SITE.

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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: 5.48 Å3/Da / Density % sol: 77.6 % / Description: NONE
Crystal growpH: 7.2
Details: 200 MM POTASSIUM FORMATE, 1.7 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: Aug 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: 3.65→54.73 Å / Num. obs: 12017 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 3.23 % / Biso Wilson estimate: 100.06 Å2 / Rsym value: 0.11 / Net I/σ(I): 9.14
Reflection shellResolution: 3.65→3.75 Å / Redundancy: 3.23 % / Mean I/σ(I) obs: 2.18 / Rsym value: 0.54 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2XDY AND 3DLB

2xdy

3dlb


Resolution: 3.65→54.73 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 23.08 / 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: Y871, L872. PDB ENTRY 2YHA WAS USED AS A REFERENCE MODEL
RfactorNum. reflection% reflection
Rfree0.252 585 4.9 %
Rwork0.233 --
obs0.234 12012 96.1 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.63 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 99.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.8575 Å20 Å20 Å2
2---1.8575 Å20 Å2
3---3.7149 Å2
Refinement stepCycle: LAST / Resolution: 3.65→54.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2880 0 11 0 2891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153087
X-RAY DIFFRACTIONf_angle_d1.2444007
X-RAY DIFFRACTIONf_dihedral_angle_d12.6031090
X-RAY DIFFRACTIONf_chiral_restr0.076445
X-RAY DIFFRACTIONf_plane_restr0.006516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6502-4.01750.32061590.27182763X-RAY DIFFRACTION96
4.0175-4.59860.2611430.23752811X-RAY DIFFRACTION96
4.5986-5.79270.22711290.2222887X-RAY DIFFRACTION97
5.7927-54.73360.2351540.22252966X-RAY DIFFRACTION95

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