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

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Basic information

Entry
Database: PDB / ID: 4nlc
TitleCrystal structure of the catalytic core of RRP6 from Trypanosoma brucei, mutant C496S
ComponentsRibosomal RNA processing protein 6
KeywordsHYDROLASE / 3'-5' exoribonuclease
Function / homology
Function and homology information


nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / 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 snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / 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 ...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
DI(HYDROXYETHYL)ETHER / Ribosomal RNA processing protein 6
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA processing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6663
Polymers42,4541
Non-polymers2122
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.410, 93.410, 49.990
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal RNA processing protein 6


Mass: 42453.711 Da / Num. of mol.: 1 / Fragment: Catalytic Domain, UNP residues 176-540 / Mutation: C496S
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG2000, pH 8.0, VAPOR DIFFUSION, SITTING 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: Jul 11, 2013
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: 2.15→50 Å / Num. obs: 19025 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 36.52 Å2 / Net I/σ(I): 9.1
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NLB

4nlb


Resolution: 2.15→48.23 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.9243 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 951 5 %RANDOM
Rwork0.1706 ---
all0.173 ---
obs0.173 19005 99.83 %-
Displacement parametersBiso mean: 38.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.5807 Å20 Å20.3893 Å2
2--0.4091 Å20 Å2
3----2.9898 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.15→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 14 212 3066
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012918HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063963HARMONIC2
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_planes416HARMONIC5
X-RAY DIFFRACTIONt_it2918HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion16.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
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_contact3591SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.27 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2531 138 4.99 %
Rwork0.2087 2625 -
all0.2107 2763 -
obs--99.83 %
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)
11.2853-0.2823-0.14860.6769-0.2950.5749-0.03070.126-0.00090.0604-0.0043-0.04890.0136-0.00240.035-0.0438-0.0213-0.0194-0.0360.0023-0.053543.6794-12.756-1.1893
23.95791.38663.11690.03190.71441.6464-0.01730.01170.0329-0.0205-0.06030.04890.0502-0.01560.07760.0486-0.0015-0.0254-0.0772-0.0178-0.076254.08258.556327.5718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|179 - A|444 }A179 - 444
2X-RAY DIFFRACTION2{ A|445 - A|540 }A445 - 540

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