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- PDB-1qcg: LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1qcg
TitleLOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN
ComponentsPOKEWEED ANTIVIRAL PROTEIN
KeywordsANTIVIRAL PROTEIN / POKEWEED ANTIVIRAL PROTEIN / RIBOSOME INACTIVATING PROTEIN / RNA SUBSTRATE ANALOGS
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: 2.1 Å
AuthorsKurinov, I.V. / Myers, D.E. / Irvin, J.D. / Uckun, F.M.
CitationJournal: 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
DepositionMay 4, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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: POKEWEED ANTIVIRAL PROTEIN
B: POKEWEED ANTIVIRAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)58,6832
Polymers58,6832
Non-polymers00
Water8,629479
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)48.680, 49.090, 64.560
Angle α, β, γ (deg.)67.950, 82.900, 65.370
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein POKEWEED ANTIVIRAL PROTEIN


Mass: 29341.467 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phytolacca americana (American pokeweed) / References: UniProt: P10297
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16-18% PEG 4000, 0.1M CACL2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
216-18 %PEG40001reservoir
30.1 M1reservoirCaCl2
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 29329 / Num. obs: 25956 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059
Reflection shellResolution: 2.1→2.17 Å / % possible obs: 78 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.137 / % possible all: 78

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -5 %random
Rwork0.191 ---
obs0.208 25077 87 %-
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 0 479 5579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.12
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 restrained with positional weight of 60 kcal/mol/A2 for main- chain atoms and 30 kcal/mol/A2 for side chain atoms. B-factor sigmas were 10 and 4 A2 for main and side chain atoms
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.12

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