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- PDB-1d6a: STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH GUANINE -

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Basic information

Entry
Database: PDB / ID: 1d6a
TitleSTRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH GUANINE
ComponentsPOKEWEED ANTIVIRAL PROTEIN
KeywordsHYDROLASE / POKEWEED ANTIVIRAL PROTEIN / 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
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
GUANINE / Antiviral protein I
Similarity search - Component
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsKurinov, I.V. / Rajamohan, F. / Venkatachalam, T.K. / Uckun, F.M.
CitationJournal: Protein Sci. / Year: 1999
Title: X-ray crystallographic analysis of the structural basis for the interaction of pokeweed antiviral protein with guanine residues of ribosomal RNA.
Authors: Kurinov, I.V. / Rajamohan, F. / Venkatachalam, T.K. / Uckun, F.M.
History
DepositionOct 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)58,9854
Polymers58,6832
Non-polymers3022
Water9,944552
1
A: POKEWEED ANTIVIRAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4932
Polymers29,3411
Non-polymers1511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POKEWEED ANTIVIRAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4932
Polymers29,3411
Non-polymers1511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.294, 49.411, 64.288
Angle α, β, γ (deg.)68.664, 81.036, 63.870
Int Tables number1
Space group name H-MP1

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Components

#1: Protein POKEWEED ANTIVIRAL PROTEIN / rRNA N-GLYCOSIDASE


Mass: 29341.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phytolacca americana (American pokeweed) / References: UniProt: P10297, rRNA N-glycosylase
#2: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16-18% PEG 4000, 0.1M CACL2, 5MM GUANINE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
222 %PEG40001reservoir
30.1 M1reservoirCaCl2
450 mMTris-HCl1reservoir
55 mMguanine1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 29, 1999 / Details: YALE DOUBLE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 29780 / Num. obs: 26047 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 1.71 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.7
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.61 % / Rmerge(I) obs: 0.158 / % possible all: 80.2
Reflection shell
*PLUS
% possible obs: 80.2 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementStarting model: 1QCI

1qci


Resolution: 2.1→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 1 / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -5 %RANDOM
Rwork0.19 ---
all0.192 ---
obs0.192 24855 --
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 28 552 5680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.97
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
Refine LS restraints NCSNCS model details: MONOMERS A AND B ARE CONNECTED BY NCS. AT THE END OF CRYSTALLOGRAPHIC REFINEMENT THE POSITIONAL RESTRAINTS BETWEEN TWO MONOMERS WERE 60 KCAL/MOL/A2 AND 30 KCAL/MOL/A2 FOR SIDE ...NCS model details: MONOMERS A AND B ARE CONNECTED BY NCS. AT THE END OF CRYSTALLOGRAPHIC REFINEMENT THE POSITIONAL RESTRAINTS BETWEEN TWO MONOMERS WERE 60 KCAL/MOL/A2 AND 30 KCAL/MOL/A2 FOR SIDE CHAINS (B-FACTOR RESTRAINTS - 10 AND 4 A2 RESPECTIVELY)
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.97

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