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- PDB-4nlb: Crystal structure of the catalytic core of RRP6 from Trypanosoma ... -

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Basic information

Entry
Database: PDB / ID: 4nlb
TitleCrystal structure of the catalytic core of RRP6 from Trypanosoma brucei
ComponentsRibosomal RNA processing protein 6
KeywordsHYDROLASE / 3'-5' exoribonuclease
Function / homology
Function and homology information


nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent CUT catabolic process / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent CUT catabolic process / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / 3'-5' exonuclease activity / rRNA processing / 3'-5'-RNA exonuclease activity / single-stranded RNA binding / nucleotide binding / nucleolus / nucleus / cytoplasm
Similarity search - Function
Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / PMC2NT (NUC016) domain / HRDC domain / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease ...Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / PMC2NT (NUC016) domain / HRDC domain / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA processing protein 6
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBarbosa, R.L. / Guimaraes, B.G.
CitationJournal: Plos One / Year: 2014
Title: RRP6 from Trypanosoma brucei: Crystal Structure of the Catalytic Domain, Association with EAP3 and Activity towards Structured and Non-Structured RNA Substrates
Authors: Barbosa, R.L. / Legrand, P. / Wien, F. / Pineau, B. / Thompson, A. / Guimaraes, B.G.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA processing protein 6


Theoretical massNumber of molelcules
Total (without water)42,4701
Polymers42,4701
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.500, 92.660, 49.910
Angle α, β, γ (deg.)90.00, 104.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal RNA processing protein 6


Mass: 42469.773 Da / Num. of mol.: 1 / Fragment: Catalytic Domain, UNP residues 176-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.4.1630 / Production host: Escherichia coli (E. coli) / References: UniProt: Q581R8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG3350, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2012
RadiationMonochromator: Channel Cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13174 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 40.42 Å2 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.8 / % possible all: 85.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20.19 Å / Cor.coef. Fo:Fc: 0.9439 / Cor.coef. Fo:Fc free: 0.9078 / SU R Cruickshank DPI: 0.706 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 656 5 %RANDOM
Rwork0.1606 ---
all0.1634 13131 --
obs0.1634 13131 96.49 %-
Displacement parametersBiso mean: 36.32 Å2
Baniso -1Baniso -2Baniso -3
1-4.8276 Å20 Å25.0693 Å2
2--3.0468 Å20 Å2
3----7.8744 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: LAST / Resolution: 2.4→20.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 0 185 3051
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012933HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.093991HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1008SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes420HARMONIC5
X-RAY DIFFRACTIONt_it2933HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion18.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion380SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3636SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.59 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2561 126 5 %
Rwork0.1777 2395 -
all0.1815 2521 -
obs--96.49 %
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)
10.97-0.139-0.08720.7915-0.08040.9148-0.0240.0431-0.04160.03560.00040.01010.047-0.0030.0236-0.0586-0.0105-0.0404-0.0478-0.0037-0.04754.3934-12.605-1.2592
21.80890.77752.72191.88911.19923.2682-0.050.02140.245-0.0625-0.10580.071-0.07630.08550.1558-0.03320.0033-0.013-0.0192-0.0336-0.082215.28699.065727.064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|176 - A|444 }A176 - 444
2X-RAY DIFFRACTION2{ A|445 - A|541 }A445 - 541

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