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- PDB-2c1w: The structure of XendoU: a splicing independent snoRNA processing... -

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Basic information

Entry
Database: PDB / ID: 2c1w
TitleThe structure of XendoU: a splicing independent snoRNA processing endoribonuclease
ComponentsENDOU PROTEIN
KeywordsNUCLEASE / SNORNA / ENDORIBONUCLEASE / SPLICING INDEPENDENT PROCESSING
Function / homology
Function and homology information


sno(s)RNA processing / RNA endonuclease activity / manganese ion binding / Lyases; Phosphorus-oxygen lyases / lyase activity / RNA binding / nucleus
Similarity search - Function
EndoU ribonuclease, C-terminal / Poly(U)-specific endoribonuclease / Endoribonuclease XendoU / Eukaryotic uridylate-specific endoribonuclease (EndoU) domain profile. / Endoribonuclease EndoU-like
Similarity search - Domain/homology
PHOSPHATE ION / Poly(U)-specific endoribonuclease-A
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsRenzi, F. / Caffarelli, E. / Laneve, P. / Bozzoni, I. / Brunori, M. / Vallone, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: The Structure of the Endoribonuclease Xendou: From Small Nucleolar RNA Processing to Severe Acute Respiratory Syndrome Coronavirus Replication.
Authors: Renzi, F. / Caffarelli, E. / Laneve, P. / Bozzoni, I. / Brunori, M. / Vallone, B.
History
DepositionSep 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOU PROTEIN
B: ENDOU PROTEIN
C: ENDOU PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0016
Polymers101,7163
Non-polymers2853
Water7,891438
1
A: ENDOU PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0002
Polymers33,9051
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDOU PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0002
Polymers33,9051
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ENDOU PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0002
Polymers33,9051
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)164.451, 53.204, 133.466
Angle α, β, γ (deg.)90.00, 121.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2026-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.903, 0.38, 0.203), (0.329, -0.305, -0.894), (-0.278, 0.874, -0.4)23.80529, 25.74303, 49.82897
2given(0.9, 0.365, -0.239), (0.356, -0.298, 0.886), (0.252, -0.882, -0.398)64.39597, -17.31528, 36.38666

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Components

#1: Protein ENDOU PROTEIN / XENDOU


Mass: 33905.223 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q8JFY9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growpH: 5.5
Details: 1.6M AMMONIUM SULPHATE, 0.2M PHOSPHATE BUFFER PH5.5, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 64530 / % possible obs: 96 % / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5, 45-53, 290-292 FROM ALL THREE NCS MONOMERS AND RESIDUES 150, 151 FROM MONOMER A, 54, 55, 288 AND 289 FROM MONOMER C WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5, 45-53, 290-292 FROM ALL THREE NCS MONOMERS AND RESIDUES 150, 151 FROM MONOMER A, 54, 55, 288 AND 289 FROM MONOMER C WERE DISORDERED AND WERE OMITTED FROM THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2463 5.1 %RANDOM
Rwork0.274 ---
obs0.274 46190 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.96 Å2
2--0.67 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 15 438 7199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9489608
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.7085864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49624.282390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.004151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7111552
X-RAY DIFFRACTIONr_chiral_restr0.1470.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025499
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.23841
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24725
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2421
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5161.54158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.17626734
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.37232948
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3314.52849
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.318 183
Rwork0.316 3232

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