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- PDB-1apa: X-RAY STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN, CODED BY A NEW G... -

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Basic information

Entry
Database: PDB / ID: 1apa
TitleX-RAY STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN, CODED BY A NEW GENOMIC CLONE, AT 0.23 NM RESOLUTION. A MODEL STRUCTURE PROVIDES A SUITABLE ELECTROSTATIC FIELD FOR SUBSTRATE BINDING.
ComponentsPOKEWEED ANTIVIRAL PROTEIN
KeywordsANTIVIRAL PROTEIN / GENOMIC CLONE
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / defense response to virus / negative regulation of translation / extracellular region
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
Antiviral protein alpha
Similarity search - Component
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsAgo, H. / Kataoka, J. / Tsuge, H. / Habuka, N. / Inagaki, E. / Noma, M. / Miyano, M.
Citation
Journal: Eur.J.Biochem. / Year: 1994
Title: X-ray structure of a pokeweed antiviral protein, coded by a new genomic clone, at 0.23 nm resolution. A model structure provides a suitable electrostatic field for substrate binding.
Authors: Ago, H. / Kataoka, J. / Tsuge, H. / Habuka, N. / Inagaki, E. / Noma, M. / Miyano, M.
#1: Journal: FEBS Lett. / Year: 1993
Title: Expression of a Pokeweed Antiviral Protein in Escherichia Coli and its Characterization
Authors: Kataoka, J. / Ago, H. / Habuka, N. / Furuno, M. / Masuta, C. / Miyano, M. / Koiwai, A.
#2: Journal: Plant Mol.Biol. / Year: 1992
Title: Isolation and Analysis of a Genomic Clone Encoding a Pokeweed Antiviral Protein
Authors: Kataoka, J. / Habuka, N. / Masuta, C. / Miyano, M. / Koiwai, A.
History
DepositionSep 21, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POKEWEED ANTIVIRAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,7661
Polymers29,7661
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.100, 116.300, 49.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO 52

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Components

#1: Protein POKEWEED ANTIVIRAL PROTEIN


Mass: 29766.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytolacca americana (American pokeweed)
References: UniProt: Q03464
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
20.2 Msodium citrate1reservoirprecipitant
321 %(v/v)PEG40001reservoirprecipitant

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 13157 / % possible obs: 98.9 % / Num. measured all: 21034 / Rmerge(I) obs: 0.068

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.172 / Rfactor obs: 0.172 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 95 2149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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