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- PDB-2a8s: 2.45 Angstrom Crystal Structure of the Complex Between the Nuclea... -

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Basic information

Entry
Database: PDB / ID: 2a8s
Title2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP
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 / 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 / snoRNA binding / cobalt ion 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
GUANOSINE-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: 2.45 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_ref_seq_dif / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _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: U8 snoRNA-binding protein X29
B: U8 snoRNA-binding protein X29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,49412
Polymers49,0082
Non-polymers1,48610
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-75 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.998, 82.553, 112.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein U8 snoRNA-binding protein X29 / E.C.3.6.1.-


Mass: 24504.127 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(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.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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 / Method: vapor diffusion, sitting drop / 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 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 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: 2.45→38.74 Å / Num. all: 17738 / Num. obs: 16302 / % possible obs: 91.9 % / Redundancy: 11.34 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.057 / Χ2: 0.97 / Net I/σ(I): 25.4 / Scaling rejects: 1398
Reflection shellResolution: 2.45→2.54 Å / % possible obs: 91.3 % / Redundancy: 10.04 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 6.9 / Num. measured obs: 78 / Num. unique all: 1737 / Χ2: 1.09 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
d*TREKdata reduction
CNSrefinement
CrystalCleardata collection
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U20

1u20


Resolution: 2.45→38.74 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.781 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS followed by restrained refinement of individual isotropic B factors.
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.631 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: refinement via simulated annealing with torsion angle dynamics as implemented in CNS v1.0 followed by Maximum likelihood refinement using REFMAC5
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1620 10 %RANDOM
Rwork0.211 ---
all0.217 17692 --
obs-16269 91.94 %-
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: 52.338 Å2
Baniso -1Baniso -2Baniso -3
1-4.5 Å20 Å20 Å2
2---1.48 Å20 Å2
3----3.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.45→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 72 48 3060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0243091
X-RAY DIFFRACTIONr_angle_refined_deg1.1392.0184163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1465383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9223.212137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20215511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4131530
X-RAY DIFFRACTIONr_chiral_restr0.0680.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022300
X-RAY DIFFRACTIONr_nbd_refined0.2010.21268
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.22
X-RAY DIFFRACTIONr_mcbond_it1.24921962
X-RAY DIFFRACTIONr_mcangle_it2.0533027
X-RAY DIFFRACTIONr_scbond_it3.39241259
X-RAY DIFFRACTIONr_scangle_it5.03561136
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 118 -
Rwork0.265 1045 -
all-1163 -
obs-1163 90.44 %
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)
12.5574-0.32970.26673.5539-0.39583.98150.145-0.6280.42450.5624-0.1994-0.1213-0.4124-0.0140.0545-0.0845-0.09570-0.0027-0.0568-0.078224.189841.62576.6797
21.6796-0.2044-0.41683.46250.6322.964-0.01510.1246-0.0254-0.26040.0116-0.1480.12190.02540.0035-0.21230.02420.0174-0.17240.0276-0.139124.071433.6556-18.197
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA18 - 20918 - 209
42BB18 - 20818 - 208

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