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- PDB-2a8r: 2.45 Angstrom Crystal Structure of the Complex Between the Nuclea... -

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Basic information

Entry
Database: PDB / ID: 2a8r
Title2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-methyl-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 / negative regulation of rRNA processing / phosphodiesterase decapping endonuclease activity ...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 / phosphodiesterase decapping endonuclease activity / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / NAD-cap decapping / 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
: / 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
: / PYROPHOSPHATE 2- / 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.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)49,6359
Polymers49,0082
Non-polymers6277
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-46 kcal/mol
Surface area16800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.200, 82.150, 112.240
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.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 14, 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
ReflectionRedundancy: 3.46 % / Av σ(I) over netI: 14.1 / Number: 754 / Rmerge(I) obs: 0.046 / Χ2: 0.99 / D res high: 2.45 Å / D res low: 23.51 Å / Num. obs: 17613 / % possible obs: 99.4 / Rejects: 460
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRejects
5.2623.5198.210.0220.99139
4.185.2699.410.0270.8662
3.664.1899.210.0380.8941
3.323.6699.710.0570.8934
3.093.3299.710.0940.9528
2.93.0999.510.1411.0243
2.762.999.710.191.0435
2.642.7699.910.2681.0629
2.542.6499.510.3161.1126
2.452.5499.510.3651.1123
ReflectionResolution: 2.45→23.51 Å / Num. all: 17716 / Num. obs: 17613 / % possible obs: 99.4 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.1
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1727 / % possible all: 99.5

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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→23 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 19.678 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS refinement followd by restrained refinement of individual B factors
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.507 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Simulated annealing via Torsion Angle Dynamics in CNS v1.0 was followed by refinement with REFMAC5,
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1739 9.9 %RANDOM
Rwork0.222 ---
all0.227 17716 --
obs-17559 99.38 %-
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: 63.01 Å2
Baniso -1Baniso -2Baniso -3
1-4.24 Å20 Å20 Å2
2---0.97 Å20 Å2
3----3.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.448 Å
Refinement stepCycle: LAST / Resolution: 2.45→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 23 73 2991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0233001
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9894049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3965385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64723.407135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00215490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6631527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022269
X-RAY DIFFRACTIONr_nbd_refined0.2110.21261
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.215
X-RAY DIFFRACTIONr_mcbond_it1.96921959
X-RAY DIFFRACTIONr_mcangle_it2.90933025
X-RAY DIFFRACTIONr_scbond_it5.08241131
X-RAY DIFFRACTIONr_scangle_it6.45761023
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 128 -
Rwork0.269 1143 -
all-1271 -
obs-1271 99.61 %
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)
13.3132-0.40.23344.1562-0.85155.66680.1848-0.86170.48410.6894-0.1802-0.1059-0.48070.1057-0.0045-0.085-0.1290.02290.0165-0.0847-0.09824.439240.97686.7496
22.34280.1212-0.75383.67120.39764.620.07630.2331-0.059-0.3226-0.0887-0.15730.1919-0.01430.0123-0.220.04790.0091-0.21350.0235-0.156624.355733.6925-18.1038
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA20 - 20920 - 209
42BB18 - 20818 - 208

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