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- PDB-2a8t: 2.1 Angstrom Crystal Structure of the Complex Between the Nuclear... -

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Basic information

Entry
Database: PDB / ID: 2a8t
Title2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A
ComponentsU8 snoRNA-binding protein X29
KeywordsTRANSLATION / HYDROLASE / 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 / negative regulation of rRNA processing / NAD-cap decapping ...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 / 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 / nucleotide binding / mRNA binding / nucleolus / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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
ADENOSINE / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / : / U8 snoRNA-decapping enzyme / U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsScarsdale, J.N. / Peculis, B.A. / Wright, H.T.
Citation
Journal: Structure / Year: 2006
Title: Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes
Authors: Scarsdale, J.N. / Peculis, B.A. / Wright, H.T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystals of X29, a Xenopus Laevis U8 SnoRNA Binding Protein with Nuclear Decapping Activity
Authors: Peculis, B.A. / Scarsdale, J.N. / Wright, H.T.
#2: Journal: Mol.Cell / Year: 2004
Title: Xenopus U8 SnoRNA Binding Protein is a Conserved Nuclear Decapping Enzyme
Authors: Ghosh, T. / Peterson, B. / Tomasevic, N. / Peculis, B.A.
History
DepositionJul 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)50,77813
Polymers48,7802
Non-polymers1,99711
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-71 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.702, 81.710, 111.706
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 / E.C.3.6.1.-


Mass: 24390.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: complexed with N-methyl-Guanosine-triphosphate-Guanosine
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DES)pLysS
References: UniProt: Q569R2, UniProt: Q6TEC1*PLUS, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#4: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 293 K / pH: 7.68
Details: 4-5 mg/ml X29, 0.025M HEPES pH 7.68, 3/75% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 3, 2005 / Details: OSMIC VARIMAX CONFOCAL OPTICS
RadiationMonochromator: OSMIC VARIMAX 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→46.17 Å / Num. obs: 27774 / % possible obs: 99.9 % / Redundancy: 6.92 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.88 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
d*TREKdata reduction
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U20

1u20


Resolution: 2.1→46.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.983 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS refinement followed by restrained refinement of individual isotropic B factors
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SIMULATED ANNEALING VIA TORSION ANGLE DYNAMICS IN CNS V1.0 WAS FOLLOWED BY MAXIMUM LIKELIHOOD REFINEMENT IN REFMAC5
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2757 9.9 %RANDOM
Rwork0.212 ---
obs0.217 27773 99.9 %-
all-27801 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20 Å2
2---0.66 Å20 Å2
3----2.96 Å2
Refine analyzeLuzzati coordinate error obs: 0.414 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 108 99 3131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0243104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1372.0284195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8835381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22923.603136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28815505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7981527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022301
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21333
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22105
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.79921957
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64333018
X-RAY DIFFRACTIONr_scbond_it4.36641307
X-RAY DIFFRACTIONr_scangle_it5.89661177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 183 -
Rwork0.261 1819 -
obs--100 %
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)
13.076-0.18830.45044.7157-0.40716.16880.0792-0.86010.51040.9452-0.2144-0.0853-0.4228-0.02680.1352-0.1506-0.12320.00350.0497-0.11-0.103524.822141.23456.8919
21.6990.445-0.61574.09791.23414.65040.0070.1261-0.0177-0.3967-0.0621-0.08730.2552-0.02570.0551-0.22230.0178-0.0008-0.23210.0314-0.15924.578933.07-18.0109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 20918 - 209
2X-RAY DIFFRACTION1AJ251 - 252
3X-RAY DIFFRACTION1AC - F300 - 303
4X-RAY DIFFRACTION2BB18 - 20818 - 208
5X-RAY DIFFRACTION2BK251 - 252
6X-RAY DIFFRACTION2BG - I304 - 306

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