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- PDB-3riu: Crystal structure of Drosophila hexameric C3PO formed by truncate... -

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Basic information

Entry
Database: PDB / ID: 3riu
TitleCrystal structure of Drosophila hexameric C3PO formed by truncated Translin and Trax
Components
  • Translin
  • Translin associated factor X, isoform B
KeywordsHYDROLASE / Translin-fold / Ribonuclease / RISC activator / Nucleus
Function / homology
Function and homology information


negative regulation of circadian sleep/wake cycle, sleep / behavioral response to starvation / Small interfering RNA (siRNA) biogenesis / RNA metabolic process / regulatory ncRNA-mediated post-transcriptional gene silencing / RNA endonuclease activity / single-stranded DNA binding / sequence-specific DNA binding / protein stabilization / protein homodimerization activity ...negative regulation of circadian sleep/wake cycle, sleep / behavioral response to starvation / Small interfering RNA (siRNA) biogenesis / RNA metabolic process / regulatory ncRNA-mediated post-transcriptional gene silencing / RNA endonuclease activity / single-stranded DNA binding / sequence-specific DNA binding / protein stabilization / protein homodimerization activity / RNA binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Translin; domain 2 / Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Translin / Translin-associated protein X / Translin-associated protein X
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsTian, Y. / Simanshu, D.K. / Patel, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex.
Authors: Tian, Y. / Simanshu, D.K. / Ascano, M. / Diaz-Avalos, R. / Park, A.Y. / Juranek, S.A. / Rice, W.J. / Yin, Q. / Robinson, C.V. / Tuschl, T. / Patel, D.J.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translin
B: Translin
C: Translin associated factor X, isoform B


Theoretical massNumber of molelcules
Total (without water)82,1013
Polymers82,1013
Non-polymers00
Water00
1
A: Translin
B: Translin
C: Translin associated factor X, isoform B

A: Translin
B: Translin
C: Translin associated factor X, isoform B


Theoretical massNumber of molelcules
Total (without water)164,2016
Polymers164,2016
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Unit cell
Length a, b, c (Å)196.030, 196.030, 155.189
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Translin / GM27569p


Mass: 25315.518 Da / Num. of mol.: 2 / Fragment: UNP residues 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG11761, Dmel_CG11761, translin, trsn
Plasmid: modified pRSFDuet-1 vector with N-terminal 6xHis and yeast sumo as fusion tag
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7JVK6
#2: Protein Translin associated factor X, isoform B / Trax


Mass: 31469.660 Da / Num. of mol.: 1 / Fragment: UNP residues 30-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel_CG5063, Trax
Plasmid: modified pRSFDuet-1 vector with N-terminal 6xHis and yeast sumo as fusion tag
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8INE1, UniProt: Q9VF77*PLUS

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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: 5.25 Å3/Da / Density % sol: 76.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.35 M-0.7 M (NH4)2HPO4, 0.1 M Na-citrate pH 5.4-5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 24690 / % possible obs: 99.8 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.214 / Net I/σ(I): 11.4
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 11 % / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2398

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.4→19.881 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.64 / σ(F): 0 / Stereochemistry target values: ML
Details: After anisotropic correction, high resolution data beyond 3.9, 3.9 and 3.4 Ang along a*, b* and c* directions, respectively, were excluded during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.3381 999 5.1 %Random
Rwork0.2705 ---
obs0.2739 19572 79.71 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.001 Å2 / ksol: 0.208 e/Å3
Displacement parametersBiso max: 365.89 Å2 / Biso mean: 96.9402 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--26.9725 Å20 Å2-0 Å2
2---26.9725 Å2-0 Å2
3----6.4379 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 0 0 4722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165118
X-RAY DIFFRACTIONf_angle_d0.8646468
X-RAY DIFFRACTIONf_chiral_restr0.062757
X-RAY DIFFRACTIONf_plane_restr0.002819
X-RAY DIFFRACTIONf_dihedral_angle_d14.7541729
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4003-3.57860.3615340.384973576922
3.5786-3.80140.3984770.35331430150744
3.8014-4.09250.37981680.30062951311990
4.0925-4.50010.3571900.269832693459100
4.5001-5.14140.28781980.247433003498100
5.1414-6.44080.35631690.30823356352599
6.4408-19.88130.29991630.216435323695100
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)
10.8682-0.4358-0.22340.15080.47460.2622-0.27390.2524-0.05340.0897-0.13030.11630.12270.22140.22670.44420.13550.23190.9678-0.03490.201882.1634102.137755.9665
20.4932-0.0673-0.33810.8612-0.2870.3821-0.0756-0.28980.0916-0.4517-0.0438-0.17010.23260.4418-0.0050.34420.33010.05470.6151-0.0940.13151.525681.336384.1377
3-0.31460.151-0.469-0.00250.11260.75270.1039-0.86390.16050.1250.1085-0.1114-0.22111.00370.11690.01240.3074-0.09031.5627-0.00820.312385.42882.795289.9005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA8 - 215
2X-RAY DIFFRACTION2chain BB7 - 213
3X-RAY DIFFRACTION3chain CC31 - 273

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