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- PDB-1pag: THE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1pag
TitleTHE 2.5 ANGSTROMS STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN
ComponentsPOKEWEED ANTIVIRAL PROTEIN
KeywordsPROTEIN SYNTHESIS INHIBITOR
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
Shiga-like toxin, subunit A / 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 ...Shiga-like toxin, subunit A / 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
FORMYCIN-5'-MONOPHOSPHATE / Antiviral protein I
Similarity search - Component
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsMonzingo, A.F. / Collins, E.J. / Ernst, S.R. / Irvin, J.D. / Robertus, J.D.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: The 2.5 A structure of pokeweed antiviral protein.
Authors: Monzingo, A.F. / Collins, E.J. / Ernst, S.R. / Irvin, J.D. / Robertus, J.D.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1977
Title: Preliminary X-Ray Diffraction Studies on an Anti-Viral Protein
Authors: Robertus, J.D. / Monzingo, A.F. / Irvin, J.D.
History
DepositionOct 19, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POKEWEED ANTIVIRAL PROTEIN
B: POKEWEED ANTIVIRAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3774
Polymers58,6832
Non-polymers6942
Water1,40578
1
A: POKEWEED ANTIVIRAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6892
Polymers29,3411
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POKEWEED ANTIVIRAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6892
Polymers29,3411
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.400, 50.100, 65.200
Angle α, β, γ (deg.)80.00, 113.20, 116.50
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES PRO A 47 AND PRO B 47 ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999686, 0.023567, 0.008488), (0.023933, -0.998656, -0.045971), (0.007393, 0.04616, -0.998907)
Vector: -1.20003, 37.58563, 62.99108)

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Components

#1: Protein POKEWEED ANTIVIRAL PROTEIN


Mass: 29341.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytolacca americana (American pokeweed)
References: UniProt: P10297
#2: Chemical ChemComp-FMP / FORMYCIN-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal grow
*PLUS
pH: 7.4 / Method: batch method
Details: Robertus, J.D., (1977) Biochem.Biophys.Res.Comm., 74, 775.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein111
20.05 MTris 11
350 %(w/v)PEG600011

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.2 / Rfactor obs: 0.2 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 46 78 4244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3
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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