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- PDB-7oc3: Crystal structure of the third tudor domain of Qin -

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Basic information

Entry
Database: PDB / ID: 7oc3
TitleCrystal structure of the third tudor domain of Qin
ComponentsQin
KeywordsPROTEIN BINDING / Tudor / Extended tudor domain / Qin
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / P granule organization / piRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / P granule / zinc ion binding / nucleus
Similarity search - Function
Tudor domain / Tudor domain profile. / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Tudor domain / Tudor domain / SNase-like, OB-fold superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...Tudor domain / Tudor domain profile. / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Tudor domain / Tudor domain / SNase-like, OB-fold superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsDhimole, N. / Klug, W. / Carlomagno, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCA 294 Germany
CitationJournal: To Be Published
Title: Crystal structure of the third tudor domain of Qin
Authors: Dhimole, N. / Klug, W. / Carlomagno, T.
History
DepositionApr 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Qin
B: Qin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4863
Polymers48,3912
Non-polymers951
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-17 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 74.800, 165.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA976 - 1187
211chain BB977 - 1185

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Components

#1: Protein Qin


Mass: 24195.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: qin, CG14303, CG14306, Dmel\CG43726, kumo, Qin, CG43726, Dmel_CG43726
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VE55
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 20% MPD

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→41.94 Å / Num. obs: 26005 / % possible obs: 99.4 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.7
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.77 / Num. unique obs: 3552

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→37.4 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.78
RfactorNum. reflection% reflection
Rfree0.2449 1335 5.15 %
Rwork0.2083 --
obs0.2102 25925 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.8 Å2 / Biso mean: 68.6744 Å2 / Biso min: 37.29 Å2
Refinement stepCycle: final / Resolution: 2.25→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 5 2 3314
Biso mean--109.07 53.61 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053385
X-RAY DIFFRACTIONf_angle_d0.9254592
X-RAY DIFFRACTIONf_chiral_restr0.039513
X-RAY DIFFRACTIONf_plane_restr0.004590
X-RAY DIFFRACTIONf_dihedral_angle_d14.5051240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1779X-RAY DIFFRACTION7.474TORSIONAL
12B1779X-RAY DIFFRACTION7.474TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.330.40261250.3123269894
2.3304-2.42370.36941500.275236098
2.4237-2.5340.32081120.26332447100
2.534-2.66750.33541200.25862459100
2.6675-2.83460.36661490.27262438100
2.8346-3.05340.31251410.25822431100
3.0534-3.36050.34261230.25012492100
3.3605-3.84630.26271470.22272473100
3.8463-4.84430.20481280.16912529100

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