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- PDB-4q5y: Crystal structure of extended-Tudor 10-11 of Drosophila melanogaster -

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Basic information

Entry
Database: PDB / ID: 4q5y
TitleCrystal structure of extended-Tudor 10-11 of Drosophila melanogaster
ComponentsMaternal protein tudor
KeywordsTRANSCRIPTION / tudor domain / recognize sDMA of Aubergine / sDMA of Aubergine / nucleus
Function / homology
Function and homology information


mitochondrial RNA localization / pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / pole plasm / methylation-dependent protein binding / P granule organization / pole plasm assembly / pole cell formation / secondary piRNA processing ...mitochondrial RNA localization / pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / pole plasm / methylation-dependent protein binding / P granule organization / pole plasm assembly / pole cell formation / secondary piRNA processing / intracellular mRNA localization / P granule / oogenesis / germ cell development / perinuclear region of cytoplasm / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #790 / : / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #790 / : / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLiu, H. / Ren, R. / Wang, W. / Wang, M. / Yang, N. / Dong, Y. / Gong, W. / Lehmann, R. / Xu, R.M.
CitationJournal: Cell Res. / Year: 2014
Title: Structure and domain organization of Drosophila Tudor
Authors: Ren, R. / Liu, H. / Wang, W. / Wang, M. / Yang, N. / Dong, Y.H. / Gong, W. / Lehmann, R. / Xu, R.M.
History
DepositionApr 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maternal protein tudor


Theoretical massNumber of molelcules
Total (without water)40,3231
Polymers40,3231
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maternal protein tudor

A: Maternal protein tudor


Theoretical massNumber of molelcules
Total (without water)80,6472
Polymers80,6472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area2060 Å2
ΔGint-10 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.247, 125.441, 151.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Maternal protein tudor


Mass: 40323.484 Da / Num. of mol.: 1 / Fragment: extended-Tudor 10-11, UNP residues 2164-2515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9450, tud, tudor / Plasmid: pET28-smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P25823
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99985 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 10, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 13994 / Num. obs: 13606 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.1
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.9 / Num. unique all: 536 / % possible all: 79.8

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTK

3ntk


Resolution: 3→50 Å / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflectionSelection details
Rfree0.271 676 RANDOM
Rwork0.236 --
all0.236 13994 -
obs0.236 12930 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 0 56 2729

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