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- PDB-4b9x: Structure of extended Tudor domain TD3 from mouse TDRD1 -

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Basic information

Entry
Database: PDB / ID: 4b9x
TitleStructure of extended Tudor domain TD3 from mouse TDRD1
ComponentsTUDOR DOMAIN-CONTAINING PROTEIN 1
KeywordsREPLICATION
Function / homology
Function and homology information


siRNA-mediated retrotransposon silencing by heterochromatin formation / pi-body / P granule organization / piRNA processing / chromatoid body / P granule / germ cell development / meiotic cell cycle / spermatogenesis / ribonucleoprotein complex ...siRNA-mediated retrotransposon silencing by heterochromatin formation / pi-body / P granule organization / piRNA processing / chromatoid body / P granule / germ cell development / meiotic cell cycle / spermatogenesis / ribonucleoprotein complex / synapse / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / : / Tudor domain / Tudor domain profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Tudor domain ...: / : / : / Tudor domain / Tudor domain profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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
Tudor domain-containing protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S.
CitationJournal: RNA / Year: 2012
Title: The Multiple Tudor Domain-Containing Protein Tdrd1 is a Molecular Scaffold for Mouse Piwi Proteins and Pirna Biogenesis Factors.
Authors: Mathioudakis, N. / Palencia, A. / Kadlec, J. / Round, A. / Tripsianes, K. / Sattler, M. / Pillai, R.S. / Cusack, S.
History
DepositionSep 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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_sheet
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_sheet.number_strands
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 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: TUDOR DOMAIN-CONTAINING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)25,3841
Polymers25,3841
Non-polymers00
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)62.960, 62.960, 132.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TUDOR DOMAIN-CONTAINING PROTEIN 1 / TDRD1


Mass: 25383.926 Da / Num. of mol.: 1 / Fragment: EXTENDED TUDOR DOMAIN TD3, RESIDUES 692-917
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q99MV1

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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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE
Crystal growTemperature: 293 K / Details: 10 % PEG 1000 AND 10 % PEG 8000 AT 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 6968 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.87 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.06 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.75 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4B9W

4b9w


Resolution: 2.8→45.63 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.194 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 1.164 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24418 330 4.7 %RANDOM
Rwork0.22281 ---
obs0.22384 6638 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.078 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 0 0 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021582
X-RAY DIFFRACTIONr_bond_other_d0.0010.021049
X-RAY DIFFRACTIONr_angle_refined_deg0.9921.9572155
X-RAY DIFFRACTIONr_angle_other_deg0.76632570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14725.06873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68115261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.745156
X-RAY DIFFRACTIONr_chiral_restr0.0570.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.804→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 20 -
Rwork0.356 390 -
obs--94.91 %

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