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- PDB-1j1q: Structure of Pokeweed Antiviral Protein from Seeds (PAP-S1) -

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Basic information

Entry
Database: PDB / ID: 1j1q
TitleStructure of Pokeweed Antiviral Protein from Seeds (PAP-S1)
ComponentsAntiviral protein S
KeywordsHYDROLASE / POKEWEED ANTIVIRAL PROTEIN / N-GLYCOSIDASE / RIBOSOME-INACTIVATING PROTEIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / defense response to virus / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWatanabe, K. / Sato, E. / Honjo, E. / Motoshima, H. / Kurokawa, H. / Mikami, B. / Monzingo, A.F. / Robertus, J.D. / Fujii, H. / Hidaka, A.
CitationJournal: To be published
Title: Crystal Structure of Pokweed Antiviral Protein from Seeds (PAP-S1) at 1.8 Angstrom Resolution
Authors: Watanabe, K. / Sato, E. / Honjo, E. / Motoshima, H. / Kurokawa, H. / Mikami, B. / Monzingo, A.F. / Robertus, J.D. / Fujii, H. / Hidaka, A.
History
DepositionDec 14, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antiviral protein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4562
Polymers29,2341
Non-polymers2211
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.100, 85.300, 92.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21A-533-

HOH

31A-534-

HOH

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Components

#1: Protein Antiviral protein S / Pokeweed Antiviral Protein / PAP-S1 / N-Glycosidase


Mass: 29234.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytolacca americana (American pokeweed) / Tissue: seeds / References: UniProt: P23339, rRNA N-glycosylase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.42 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 66% Saturated Ammomium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→9 Å / Num. all: 26149 / Num. obs: 26149 / Observed criterion σ(F): 0 / Biso Wilson estimate: 11.5 Å2 / Limit h max: 43 / Limit h min: 0 / Limit k max: 47 / Limit k min: 0 / Limit l max: 51 / Limit l min: 0 / Observed criterion F max: 1605946.28 / Observed criterion F min: 6.7

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
X-PLORphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→9 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2587 9.9 %random
Rwork0.173 ---
all-29084 --
obs-26149 89.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 78.4914 Å2 / ksol: 0.224625 e/Å3
Displacement parametersBiso max: 86.5 Å2 / Biso mean: 24.03 Å2 / Biso min: 7.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.76 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.32 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 14 238 2305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_torsion_deg24.1
X-RAY DIFFRACTIONx_torsion_impr_deg1.04
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.3242249.60.32321010.0223606232564.5
1.88-1.980.3042699.80.26724820.0193604275176.3
1.98-2.10.263039.50.23528900.0153594319388.8
2.1-2.260.256341100.20730830.0143620342494.6
2.26-2.490.2437510.70.18831440.0123631351996.9
2.49-2.840.2213349.40.17432210.0123628355598
2.84-3.540.2023539.70.14732850.0113671363899.1
3.54-90.19538810.40.11933560.013760374499.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top

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