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- PDB-1wdy: Crystal structure of ribonuclease -

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Basic information

Entry
Database: PDB / ID: 1wdy
TitleCrystal structure of ribonuclease
Components2-5A-dependent ribonuclease
KeywordsHYDROLASE / Nuclease / RNA-binding
Function / homology
Function and homology information


OAS antiviral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / negative regulation of viral genome replication / fat cell differentiation / RNA nuclease activity / RNA processing / ribonucleoprotein complex binding / RNA endonuclease activity / regulation of mRNA stability / positive regulation of glucose import ...OAS antiviral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / negative regulation of viral genome replication / fat cell differentiation / RNA nuclease activity / RNA processing / ribonucleoprotein complex binding / RNA endonuclease activity / regulation of mRNA stability / positive regulation of glucose import / mRNA processing / rRNA processing / nuclear matrix / Interferon alpha/beta signaling / defense response to virus / rRNA binding / mitochondrial matrix / protein kinase activity / protein phosphorylation / positive regulation of transcription by RNA polymerase II / RNA binding / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
RNase L, RNase domain / Ankyrin repeats (many copies) / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) ...RNase L, RNase domain / Ankyrin repeats (many copies) / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Chem-25A / 2-5A-dependent ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTanaka, N. / Nakanishi, M. / Kusakabe, Y. / Goto, Y. / Kitade, Y. / Nakamura, K.T.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis for recognition of 2',5'-linked oligoadenylates by human ribonuclease L
Authors: Tanaka, N. / Nakanishi, M. / Kusakabe, Y. / Goto, Y. / Kitade, Y. / Nakamura, K.T.
History
DepositionMay 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _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

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Assembly

Deposited unit
A: 2-5A-dependent ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1822
Polymers31,1771
Non-polymers1,0061
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.203, 72.834, 82.634
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 2-5A-dependent ribonuclease / 2-5A-dependent RNase / Ribonuclease L / RNase L / Ribonuclease 4


Mass: 31176.789 Da / Num. of mol.: 1 / Fragment: residues 21-305 / Mutation: I97K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q05823, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-25A / 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE


Mass: 1005.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38N15O19P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, sodium acetate, glycerol, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 35922 / % possible obs: 99.7 %
Reflection shellResolution: 1.8→1.9 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.316 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22994 1791 5 %RANDOM
Rwork0.20178 ---
obs0.2032 34084 99.53 %-
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: 25.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 67 220 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212283
X-RAY DIFFRACTIONr_bond_other_d0.0020.022109
X-RAY DIFFRACTIONr_angle_refined_deg1.1192.0173085
X-RAY DIFFRACTIONr_angle_other_deg0.7734916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9975284
X-RAY DIFFRACTIONr_chiral_restr0.0620.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022499
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02402
X-RAY DIFFRACTIONr_nbd_refined0.2390.2523
X-RAY DIFFRACTIONr_nbd_other0.2210.22472
X-RAY DIFFRACTIONr_nbtor_other0.0790.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.211
X-RAY DIFFRACTIONr_mcbond_it0.6691.51406
X-RAY DIFFRACTIONr_mcangle_it1.29522233
X-RAY DIFFRACTIONr_scbond_it1.8253877
X-RAY DIFFRACTIONr_scangle_it3.0844.5852
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 123
Rwork0.259 2482

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