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

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Basic information

Entry
Database: PDB / ID: 1paf
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
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,6832
Polymers58,6832
Non-polymers00
Water1,56787
1
A: POKEWEED ANTIVIRAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,3411
Polymers29,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POKEWEED ANTIVIRAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,3411
Polymers29,3411
Non-polymers00
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: (0.998879, 0.026261, 0.039393), (0.02807, -0.998542, -0.046099), (0.038125, 0.047153, -0.99816)
Vector: -1.77508, 37.54194, 62.62427)

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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-ID
140 mg/mlprotein11
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: 0.17 / Rfactor obs: 0.17 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 0 87 4207
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_deg3.6
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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