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- PDB-1lln: 1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III... -

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Basic information

Entry
Database: PDB / ID: 1lln
Title1.6A CRYSTAL STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN-III (PAP-III) WITH METHYLATED LYSINES
ComponentsAntiviral Protein 3
KeywordsHYDROLASE / POKEWEED ANTIVIRAL PROTEIN / RIBOSOME INACTIVATING PROTEIN / POLYNUCLEOTIDE:ADENOSINE
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
Antiviral protein II/III
Similarity search - Component
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKurinov, I.V. / Uckun, F.M.
Citation
Journal: Biochem.Pharm. / Year: 2003
Title: High resolution X-ray structure of potent anti-HIV pokeweed antiviral protein-III
Authors: Kurinov, I.V. / Uckun, F.M.
#1: Journal: Protein Sci. / Year: 1999
Title: X-Ray Crystallographic Analysis of the Structural Basis for the Interactions of Pokeweed Antiviral Protein with its Active Site Inhibitor and Ribosomal RNA Substrate Analogs
Authors: Kurinov, I.V. / Myers, D.E. / Irvin, J.D. / Uckun, F.M.
History
DepositionApr 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antiviral Protein 3


Theoretical massNumber of molelcules
Total (without water)29,6831
Polymers29,6831
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.47, 80.47, 76.21
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Antiviral Protein 3 / PAP-II / Ribosome-inactivating protein / rRNA N-glycosidase


Mass: 29683.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: late summer leaves / Source: (natural) Phytolacca americana (American pokeweed) / References: UniProt: Q40772, rRNA N-glycosylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.3 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 30% PEG400, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.2 Msodium borate1reservoirpH8.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 38088 / Num. obs: 37018 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.9
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.132 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 1.6 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→7 Å / Data cutoff low absF: 0.0001 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3605 10 %RANDOM
Rwork0.201 ---
obs0.203 36455 97.1 %-
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 0 260 2357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.67
X-RAY DIFFRACTIONx_improper_angle_d1.17
Refinement
*PLUS
Highest resolution: 1.6 Å / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17

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