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- PDB-5gvd: Human TDRD3 DUF1767-OB domains -

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Basic information

Entry
Database: PDB / ID: 5gvd
TitleHuman TDRD3 DUF1767-OB domains
ComponentsTudor domain-containing protein 3
KeywordsPROTEIN BINDING / scaffold protein
Function / homology
Function and homology information


DNA topoisomerase III-beta-TDRD3 complex / DNA topological change / methylated histone binding / chromatin organization / transcription coactivator activity / chromatin binding / Golgi apparatus / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Tudor domain-containing protein 3, UBA domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Tudor domain / Tudor domain profile. / UBA/TS-N domain / Tudor domain / Tudor domain ...: / Tudor domain-containing protein 3, UBA domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Tudor domain / Tudor domain profile. / UBA/TS-N domain / Tudor domain / Tudor domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.623 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Takahashi, T.S. / Fukai, S.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Authors: Goto-Ito, S. / Yamagata, A. / Takahashi, T.S. / Sato, Y. / Fukai, S.
History
DepositionSep 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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
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: Tudor domain-containing protein 3
B: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9578
Polymers35,5572
Non-polymers4006
Water4,342241
1
A: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8732
Polymers17,7781
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-4 kcal/mol
Surface area8580 Å2
MethodPISA
2
B: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0846
Polymers17,7781
Non-polymers3055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.669, 85.669, 104.207
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tudor domain-containing protein 3


Mass: 17778.318 Da / Num. of mol.: 2 / Fragment: UNP residues 1-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7E2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.26 M NaH2PO4 and 0.14 M K2HPO4 (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 54685 / % possible obs: 100 % / Redundancy: 20.4 % / Net I/σ(I): 43.9
Reflection shellResolution: 1.62→1.65 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NBI

3nbi


Resolution: 1.623→42.834 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.1989 2775 5.07 %
Rwork0.1746 --
obs0.1758 54684 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.623→42.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 23 241 2578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182410
X-RAY DIFFRACTIONf_angle_d1.6073268
X-RAY DIFFRACTIONf_dihedral_angle_d13.871906
X-RAY DIFFRACTIONf_chiral_restr0.097389
X-RAY DIFFRACTIONf_plane_restr0.008414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6231-1.6510.26441560.23772578X-RAY DIFFRACTION99
1.651-1.68110.26861250.22662592X-RAY DIFFRACTION100
1.6811-1.71340.26941260.22292598X-RAY DIFFRACTION100
1.7134-1.74840.24241120.20912611X-RAY DIFFRACTION100
1.7484-1.78640.23481510.20532564X-RAY DIFFRACTION100
1.7864-1.8280.21611400.19312606X-RAY DIFFRACTION100
1.828-1.87370.20721430.19352584X-RAY DIFFRACTION100
1.8737-1.92430.24691310.2042568X-RAY DIFFRACTION100
1.9243-1.98090.25291350.19462608X-RAY DIFFRACTION100
1.9809-2.04490.23651360.19132598X-RAY DIFFRACTION100
2.0449-2.1180.21811590.18522569X-RAY DIFFRACTION100
2.118-2.20280.18151340.1742603X-RAY DIFFRACTION100
2.2028-2.3030.18691500.17312569X-RAY DIFFRACTION100
2.303-2.42440.21011270.17592601X-RAY DIFFRACTION100
2.4244-2.57630.19461560.17542575X-RAY DIFFRACTION100
2.5763-2.77520.19411460.18152605X-RAY DIFFRACTION100
2.7752-3.05440.19151210.18052620X-RAY DIFFRACTION100
3.0544-3.49620.21161600.16482572X-RAY DIFFRACTION100
3.4962-4.40410.15271410.14612624X-RAY DIFFRACTION100
4.4041-42.84940.17771260.15642664X-RAY DIFFRACTION100

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