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- PDB-1wlj: human ISG20 -

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Basic information

Entry
Database: PDB / ID: 1wlj
Titlehuman ISG20
Componentsinterferon stimulated gene 20kDa
KeywordsHYDROLASE / exoribonuclease
Function / homology
Function and homology information


exoribonuclease II / exoribonuclease II activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / RNA catabolic process / U3 snoRNA binding / exonuclease activity / negative regulation of viral genome replication / Cajal body / U2 snRNA binding ...exoribonuclease II / exoribonuclease II activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / RNA catabolic process / U3 snoRNA binding / exonuclease activity / negative regulation of viral genome replication / Cajal body / U2 snRNA binding / U1 snRNA binding / P-body / response to virus / PML body / rRNA processing / Interferon alpha/beta signaling / 3'-5'-RNA exonuclease activity / defense response to virus / innate immune response / nucleolus / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / URIDINE-5'-MONOPHOSPHATE / : / Interferon-stimulated gene 20 kDa protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD with data collected at 1.0085, 1.005, 0.92 A / Resolution: 1.9 Å
AuthorsHorio, T. / Murai, M. / Inoue, T. / Hamasaki, T. / Tanaka, T. / Ohgi, T.
CitationJournal: Febs Lett. / Year: 2004
Title: Crystal structure of human ISG20, an interferon-induced antiviral ribonuclease
Authors: Horio, T. / Murai, M. / Inoue, T. / Hamasaki, T. / Tanaka, T. / Ohgi, T.
History
DepositionJun 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_dist_value / _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_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
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: interferon stimulated gene 20kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0176
Polymers21,4691
Non-polymers5485
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.420, 63.420, 97.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein interferon stimulated gene 20kDa / interferon stimulated gene product of 20kDa / interferon stimulated gene (20kD)


Mass: 21468.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: GenBank: 6857800, UniProt: Q96AZ6*PLUS, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium acetate, sodium chloride, 1-butanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→55 Å / Num. obs: 18442 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.039

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
CNXrefinement
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: MAD with data collected at 1.0085, 1.005, 0.92 A
Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 937 -random
Rwork0.207 ---
obs-18424 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 28 79 1420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_deg1.2

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