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- PDB-2wac: Extended Tudor domain of Drosophila Melanogaster Tudor-SN (p100) -

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Basic information

Entry
Database: PDB / ID: 2wac
TitleExtended Tudor domain of Drosophila Melanogaster Tudor-SN (p100)
ComponentsCG7008-PA
KeywordsSPLICING / UNKNOWN FUNCTION / TUDOR / BETA-BARREL / NUCLEASE DOMAIN / TUDOR-SN / P100 / SND1 / METHYLATED ARGININE / SDMA
Function / homology
Function and homology information


: / nuclease activity / regulatory ncRNA-mediated gene silencing / RNA catabolic process / RISC complex / micrococcal nuclease / spermatogenesis / endonuclease activity / RNA binding / nucleus ...: / nuclease activity / regulatory ncRNA-mediated gene silencing / RNA catabolic process / RISC complex / micrococcal nuclease / spermatogenesis / endonuclease activity / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. ...RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Staphylococcal nuclease domain-containing protein 1
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFriberg, A. / Corsini, L. / Sattler, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and Ligand Binding of the Extended Tudor Domain of D. Melanogaster Tudor-Sn
Authors: Friberg, A. / Corsini, L. / Mourao, A. / Sattler, M.
History
DepositionFeb 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG7008-PA
B: CG7008-PA


Theoretical massNumber of molelcules
Total (without water)48,4672
Polymers48,4672
Non-polymers00
Water5,459303
1
A: CG7008-PA


Theoretical massNumber of molelcules
Total (without water)24,2331
Polymers24,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CG7008-PA


Theoretical massNumber of molelcules
Total (without water)24,2331
Polymers24,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.560, 47.040, 129.770
Angle α, β, γ (deg.)90.00, 107.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CG7008-PA / LD20211P / TUDOR-SN


Mass: 24233.254 Da / Num. of mol.: 2 / Fragment: TSN DOMAIN, TUDOR AND SN5, RESIDUES 700-916
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9W0S7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 6.8 / Details: 20% PEG 3350, 100 MM BIS-TRIS PH 5.5, 200 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179
DetectorDate: Jun 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→19.64 Å / Num. obs: 28296 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 3.63 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.4
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 3.51 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 10.2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HQE

2hqe


Resolution: 2.1→19.64 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.159 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1415 5 %RANDOM
Rwork0.227 ---
obs0.229 26881 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20.48 Å2
2---0.88 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 0 303 3687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.9684647
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70625.226155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03415577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7371518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21304
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.290.22346
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2261
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3061.52233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.3923470
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.46731353
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.784.51175
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 102 -
Rwork0.251 1945 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.98920.1821-2.92620.9884-0.1565.0340.1118-0.19270.06030.0094-0.0301-0.1222-0.19220.5951-0.08170.00650.01770.0335-0.07060.0215-0.118626.138-25.9927.483
20.9380.446-1.68350.8817-0.60273.69190.01920.06830.0118-0.0926-0.01440.04610.0795-0.0247-0.0048-0.01660.0340.0447-0.14160.0075-0.180417.887-29.1167.024
32.2097-0.26120.19992.5642-0.53422.01120.0453-0.0196-0.07710.02130.02530.23750.0319-0.2636-0.07060.0024-0.00240.0633-0.14590.0142-0.1342-0.461-30.94724.006
47.08012.4494-0.58117.95520.22013.01510.0935-0.06610.1661-0.0825-0.05050.4403-0.1299-0.2223-0.04310.13560.00010.0775-0.11340.0182-0.1907-7.202-3.94446.343
50.5-0.75711.647611.5589-4.18415.7040.11520.0624-0.18892.3412-0.1339-0.0309-0.8481-0.14770.01870.9898-0.1050.1752-0.03340.0013-0.0683-4.001-3.61768.636
60.8766-0.0491-0.5193.5723-0.2613.50260.0612-0.0721-0.0840.1483-0.05740.23610.0238-0.059-0.00380.0612-0.01710.019-0.1590.0076-0.1077-2.03-7.0342.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A699 - 756
2X-RAY DIFFRACTION2A757 - 861
3X-RAY DIFFRACTION3A862 - 914
4X-RAY DIFFRACTION4B699 - 721
5X-RAY DIFFRACTION5B722 - 778
6X-RAY DIFFRACTION6B779 - 914

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