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- PDB-1u20: Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRN... -

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Basic information

Entry
Database: PDB / ID: 1u20
TitleCrystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29
ComponentsU8 snoRNA-binding protein X29
KeywordsHYDROLASE / modified Nudix hydrolase fold
Function / homology
Function and homology information


inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD+-cap (NAD+-forming) hydrolase activity / dITP diphosphatase activity / phosphodiesterase decapping endonuclease activity / negative regulation of rRNA processing ...inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD+-cap (NAD+-forming) hydrolase activity / dITP diphosphatase activity / phosphodiesterase decapping endonuclease activity / negative regulation of rRNA processing / NAD-cap decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / metalloexopeptidase activity / cobalt ion binding / snoRNA binding / mRNA catabolic process / manganese ion binding / mRNA binding / nucleotide binding / nucleolus / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / U8 snoRNA-decapping enzyme-like / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsScarsdale, J.N. / Peculis, B.A. / Wright, H.T.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29
Authors: Scarsdale, J.N. / Peculis, B.A. / Wright, H.T.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Downloads & links

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Assembly

Deposited unit
A: U8 snoRNA-binding protein X29
B: U8 snoRNA-binding protein X29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9644
Polymers48,7802
Non-polymers1842
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-20 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.188, 82.990, 111.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein U8 snoRNA-binding protein X29


Mass: 24390.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6TEC1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.27 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.68
Details: 0.025 M HEPES, 3.75% PEG 6000, pH 7.68, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 20, 2004 / Details: Osmic Confocal optics
RadiationMonochromator: Osmic confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→26.8 Å / Num. all: 27307 / Num. obs: 27224 / Redundancy: 6.8 % / Biso Wilson estimate: 46.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 7.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.355 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→26.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.772 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25421 2701 9.9 %RANDOM
Rwork0.20404 ---
obs0.20881 24464 99.68 %-
all-27273 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.719 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2---1.18 Å20 Å2
3----1.23 Å2
Refine analyzeLuzzati coordinate error obs: 0.287 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 11 186 3234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213141
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.984232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7715392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21413
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.861.51948
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60323107
X-RAY DIFFRACTIONr_scbond_it2.08431193
X-RAY DIFFRACTIONr_scangle_it3.4984.51125
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 218
Rwork0.241 1717
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)
10.957-0.16120.16811.29390.06881.49360.0696-0.1940.12610.1947-0.1238-0.0756-0.0856-0.09140.05420.0402-0.03690.01250.0344-0.01580.04823.509940.47996.2343
20.57150.0284-0.21851.38460.28731.17390.0570.0969-0.0033-0.1251-0.0896-0.0302-0.0001-0.07790.03260.04220.02320.02530.02810.01810.040922.78335.3013-17.0434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 20933 - 209
2X-RAY DIFFRACTION2BB33 - 20833 - 208

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