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- PDB-3ntk: Crystal structure of Tudor -

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Basic information

Entry
Database: PDB / ID: 3ntk
TitleCrystal structure of Tudor
ComponentsMaternal protein tudor
KeywordsTRANSCRIPTION / Tudor domain / OB-fold / germ cell formation
Function / homology
Function and homology information


pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / methylation-dependent protein binding / pole plasm / secondary piRNA processing / P granule organization / pole plasm assembly / pole cell formation / piRNA processing ...pole cell development / positive regulation of post-transcriptional gene silencing by RNA / P granule assembly / methylation-dependent protein binding / pole plasm / secondary piRNA processing / P granule organization / pole plasm assembly / pole cell formation / piRNA processing / intracellular mRNA localization / P granule / oogenesis / germ cell development / spermatogenesis / 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
Maternal protein tudor
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsLiu, H.P. / Huang, Y. / Li, Z.Z. / Gong, W.M. / Xu, R.M.
CitationJournal: Genes Dev. / Year: 2010
Title: Structural basis for methylarginine-dependent recognition of Aubergine by Tudor
Authors: Liu, H.P. / Wang, J.Y. / Huang, Y. / Li, Z.Z. / Gong, W.M. / Lehmann, R. / Xu, R.M.
History
DepositionJul 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maternal protein tudor
B: Maternal protein tudor


Theoretical massNumber of molelcules
Total (without water)38,3952
Polymers38,3952
Non-polymers00
Water3,351186
1
A: Maternal protein tudor


Theoretical massNumber of molelcules
Total (without water)19,1981
Polymers19,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maternal protein tudor


Theoretical massNumber of molelcules
Total (without water)19,1981
Polymers19,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.145, 47.262, 85.404
Angle α, β, γ (deg.)90.00, 106.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Maternal protein tudor


Mass: 19197.617 Da / Num. of mol.: 2 / Fragment: the last extended Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: tud / Plasmid: pET-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P25823
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.0809
SYNCHROTRONNSLS X12C20.9790, 0.9792, 0.9600
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.08091
20.9791
30.97921
40.961
ReflectionResolution: 1.8→50 Å / Num. obs: 35907 / % possible obs: 96.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2970 / % possible all: 80.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8535 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2378 3580 9.6 %
Rwork0.2101 --
obs-35864 96.2 %
Solvent computationBsol: 48.1193 Å2
Displacement parametersBiso max: 61.88 Å2 / Biso mean: 31.2326 Å2 / Biso min: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.763 Å20 Å2-4.699 Å2
2---1.814 Å20 Å2
3---7.577 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 0 186 2852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.382
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.810.3419470.2729462509
1.81-1.820.2832520.2781521573
1.82-1.840.3081660.2692541607
1.84-1.850.2811580.2531565623
1.85-1.860.2968540.2802594648
1.86-1.880.2675650.2605613678
1.88-1.890.2895770.2368594671
1.89-1.910.2331710.2439669740
1.91-1.920.1952800.2165610690
1.92-1.940.2831620.2061660722
1.94-1.960.2267680.2234694762
1.96-1.970.2697750.2307656731
1.97-1.990.1975740.211641715
1.99-2.010.2612770.2046642719
2.01-2.030.2365700.2089666736
2.03-2.050.2232670.2126692759
2.05-2.070.1822840.1978636720
2.07-2.090.2112780.2066656734
2.09-2.110.2363670.1997664731
2.11-2.130.2669690.2038671740
2.13-2.160.2028680.1996665733
2.16-2.180.263700.2141663733
2.18-2.210.2404940.2083653747
2.21-2.240.2638910.2191647738
2.24-2.270.2663790.2151664743
2.27-2.30.2596740.2131660734
2.3-2.330.2283700.1887659729
2.33-2.370.3075710.2285694765
2.37-2.40.2464650.218642707
2.4-2.440.2466880.1982680768
2.44-2.490.2198710.2167679750
2.49-2.530.2497720.2298642714
2.53-2.580.2625660.2358669735
2.58-2.630.2637820.243680762
2.63-2.690.2543690.2248638707
2.69-2.750.2558670.2374695762
2.75-2.820.2429650.2278667732
2.82-2.90.2522910.2223652743
2.9-2.980.3034780.2157658736
2.98-3.080.2113630.2051675738
3.08-3.190.2383680.2255695763
3.19-3.320.2153770.2097640717
3.32-3.470.1883730.2007667740
3.47-3.650.2532720.1989670742
3.65-3.880.2299650.1904674739
3.88-4.180.2212750.1661633708
4.18-4.60.2068690.1704668737
4.6-5.260.202730.1742678751
5.26-6.630.2734810.2519671752
6.63-500.2456720.2618559631
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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