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- PDB-3pmt: Crystal structure of the Tudor domain of human Tudor domain-conta... -

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Basic information

Entry
Database: PDB / ID: 3pmt
TitleCrystal structure of the Tudor domain of human Tudor domain-containing protein 3
ComponentsTudor domain-containing protein 3
KeywordsTRANSCRIPTION / Tudor domain / Structural Genomics Consortium / SGC / sulfur phasing / Nucleus
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 / SH3 type barrels. - #140 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsLam, R. / Bian, C.B. / Guo, Y.H. / Xu, C. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Lam, R. / Bian, C.B. / Guo, Y.H. / Xu, C. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30.
Authors: Liu, K. / Guo, Y. / Liu, H. / Bian, C. / Lam, R. / Liu, Y. / Mackenzie, F. / Rojas, L.A. / Reinberg, D. / Bedford, M.T. / Xu, R.M. / Min, J.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5May 31, 2023Group: Database references / Derived calculations / Category: database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tudor domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0782
Polymers6,8841
Non-polymers1941
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.682, 41.682, 59.947
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tudor domain-containing protein 3


Mass: 6883.764 Da / Num. of mol.: 1 / Fragment: Tudor domain, UNP residues 553-611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9H7E2
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 2.0M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 12, 2010 / Details: VariMax HF
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 5478 / % possible obs: 98.7 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.031 / Χ2: 1.108 / Net I/σ(I): 35.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.848.50.0993140.913185.8
1.84-1.8911.60.0983580.833197.5
1.89-1.9415.70.0893531.036197.5
1.94-218.20.0783771.1081100
2-2.0620.10.0723621.1161100
2.06-2.1320.80.0643681.181100
2.13-2.2221.40.0553691.1391100
2.22-2.3221.60.0543701.1251100
2.32-2.4421.80.0463701.1091100
2.44-2.621.90.0423691.1561100
2.6-2.821.90.0363661.1391100
2.8-3.08220.033661.0991100
3.08-3.5222.10.0253731.1211100
3.52-4.44220.0223771.0491100
4.44-50210.0213861.209199

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.8 Å / D res low: 19.69 Å / FOM acentric: 0.247 / FOM centric: 0.073 / Reflection acentric: 5214 / Reflection centric: 232
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.819.69005214232
ANO_11.819.690.749051790
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_16.79-19.69008816
ISO_14.95-6.790015315
ISO_14.08-4.950019114
ISO_13.56-4.080023516
ISO_13.19-3.560025714
ISO_12.92-3.190029416
ISO_12.71-2.920031215
ISO_12.54-2.710034316
ISO_12.39-2.540035213
ISO_12.27-2.390038117
ISO_12.17-2.270040515
ISO_12.08-2.170041314
ISO_12-2.080044115
ISO_11.92-20045016
ISO_11.86-1.920046610
ISO_11.8-1.860043310
ANO_16.79-19.691.6210880
ANO_14.95-6.791.57601530
ANO_14.08-4.951.03701910
ANO_13.56-4.081.00502350
ANO_13.19-3.560.97802570
ANO_12.92-3.190.99502940
ANO_12.71-2.920.92103120
ANO_12.54-2.710.97203430
ANO_12.39-2.540.86303520
ANO_12.27-2.390.78403810
ANO_12.17-2.270.64804050
ANO_12.08-2.170.5504130
ANO_12-2.080.49404410
ANO_11.92-20.36504480
ANO_11.86-1.920.28904600
ANO_11.8-1.860.19304060
Phasing MAD set siteCartn x: 13.529 Å / Cartn y: 14.745 Å / Cartn z: 10.011 Å / Atom type symbol: S / B iso: 24.53 / Occupancy: 1.63
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
6.79-19.690.5170.1328816
4.95-6.790.4530.07115315
4.08-4.950.3920.07819114
3.56-4.080.3540.05623516
3.19-3.560.3770.07825714
2.92-3.190.3680.08729416
2.71-2.920.3410.09531215
2.54-2.710.30.08734316
2.39-2.540.2650.07435213
2.27-2.390.2450.05438117
2.17-2.270.2010.08940515
2.08-2.170.1920.0441314
2-2.080.1740.04644115
1.92-20.1520.0645016
1.86-1.920.1210.04846610
1.8-1.860.1170.04643310
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 5446
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
4.02-10069.40.899506
3.18-4.0271.80.94503
2.78-3.1870.50.92503
2.52-2.7868.30.911504
2.34-2.5266.70.922505
2.2-2.3470.20.926508
2.09-2.282.10.922501
2-2.0979.50.919502
1.92-279.90.916502
1.8-1.9283.10.843912

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6.1phasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.203 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 247 4.5 %RANDOM
Rwork0.1775 ---
obs0.1789 5444 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.82 Å2 / Biso mean: 26.4207 Å2 / Biso min: 14.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms447 0 10 36 493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022474
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.95641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.258556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83524.78323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4721574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.373151
X-RAY DIFFRACTIONr_chiral_restr0.0840.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.242210.18832539487.817
1.847-1.8970.19160.19436940096.25
1.897-1.9510.214150.17335837499.733
1.951-2.0110.254110.159363374100
2.011-2.0760.289180.185347365100
2.076-2.1480.206150.185325340100
2.148-2.2280.206220.178316338100
2.228-2.3180.177100.194317327100
2.318-2.4190.225130.192298311100
2.419-2.5360.27160.194274290100
2.536-2.670.221180.192274292100
2.67-2.8290.198120.186255267100
2.829-3.020.26120.193245257100
3.02-3.2560.2480.196226234100
3.256-3.5570.24390.166208217100
3.557-3.960.126100.149189199100
3.96-4.5420.07640.136175179100
4.542-5.4910.11860.15146152100
5.491-7.4790.20560.228114120100
7.479-19.6850.43950.205737998.734
Refinement TLS params.Method: refined / Origin x: 14.641 Å / Origin y: 11.004 Å / Origin z: 4.052 Å
111213212223313233
T0.0219 Å20.008 Å20.0062 Å2-0.0259 Å2-0.0034 Å2--0.0096 Å2
L1.0777 °2-0.1404 °21.3221 °2-2.5698 °2-0.2574 °2--2.4387 °2
S-0.0508 Å °0.0001 Å °-0.0208 Å °-0.048 Å °0.0332 Å °-0.04 Å °-0.1117 Å °0.0122 Å °0.0176 Å °

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