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- PDB-2a8q: 2.6 Angstrom Crystal Structure of the Complex Between the Nuclear... -

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Basic information

Entry
Database: PDB / ID: 2a8q
Title2.6 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-methyl-GDP
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: 2.6 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)49,3458
Polymers48,8942
Non-polymers4516
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-47 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.828, 82.284, 111.860
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: 24447.076 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.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: Aug 23, 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: 2.6→29.85 Å / Num. all: 14734 / Num. obs: 14707 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 73.8 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 8.9
Reflection shellResolution: 2.6→2.67 Å / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 1071 / Num. unique all: 1071 / Rsym value: 0.433 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U20

1u20


Resolution: 2.6→27.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 22.428 / SU ML: 0.228 / 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: 0.985 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Initial refinement with sumulated annealing using torsion angle dynamics in CNS v1.0 followed by refinement in Refmac5
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1443 10.1 %RANDOM
Rwork0.202 ---
all0.208 14735 --
obs-14223 96.81 %-
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: 60.844 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å20 Å20 Å2
2---0.74 Å20 Å2
3----3.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.464 Å
Refinement stepCycle: LAST / Resolution: 2.6→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 14 44 2958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222963
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9874002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.085378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96123.534133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41315492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9051526
X-RAY DIFFRACTIONr_chiral_restr0.0710.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022238
X-RAY DIFFRACTIONr_nbd_refined0.2070.21246
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.213
X-RAY DIFFRACTIONr_mcbond_it1.71521943
X-RAY DIFFRACTIONr_mcangle_it2.77332998
X-RAY DIFFRACTIONr_scbond_it4.44941109
X-RAY DIFFRACTIONr_scangle_it6.40561004
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 109 -
Rwork0.345 886 -
all-995 -
obs-995 94.05 %
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)
13.9516-0.73470.52365.3113-1.21165.87470.1461-0.910.62980.8331-0.1573-0.0951-0.5483-0.1080.0112-0.0816-0.13650.0286-0.0316-0.0738-0.141424.140.91766.6923
22.35090.2881-0.36624.73160.56244.24290.0510.273-0.055-0.4767-0.0545-0.16890.1448-0.04990.0035-0.16930.04720.0376-0.19070.0431-0.193624.172333.8519-18.0826
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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