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- PDB-1lpc: HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTE... -

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Basic information

Entry
Database: PDB / ID: 1lpc
TitleHIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTEIN-POTENT ANTI-HIV AGENT (COMPLEX WITH CYCLIC AMP)
ComponentsDIANTHIN 30
KeywordsANTIVIRAL PROTEIN / DIANTHIN ANTIVIRAL PROTEIN / RIBOSOME INACTIVATING PROTEIN / ANTI-HIV AGENT / HIV-1 INTEGRASE INHIBITOR / POLYNUCLEOTIDE:ADENOSINE GLYCOSIDASE
Function / homology
Function and homology information


regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / 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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Ribosome-inactivating protein dianthin-30
Similarity search - Component
Biological speciesDianthus caryophyllus (clove pink)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKurinov, I.V. / Rajamohan, F. / Uckun, F.M.
CitationJournal: Arzneimittelforschung / Year: 2004
Title: High resolution X-ray structure and potent anti-HIV activity of recombinant dianthin antiviral protein.
Authors: Kurinov, I.V. / Rajamohan, F. / Uckun, F.M.
History
DepositionMay 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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Assembly

Deposited unit
A: DIANTHIN 30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9332
Polymers28,6041
Non-polymers3291
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.122, 78.498, 42.715
Angle α, β, γ (deg.)90., 105.228, 90.
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DIANTHIN 30 / Antiviral protein DAP-30 / rRNA N-glycosylase / rRNA N-glycosidase / Ribosome-inactivating protein


Mass: 28603.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dianthus caryophyllus (clove pink) / Production host: Escherichia coli (E. coli) / References: UniProt: P24476, rRNA N-glycosylase
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% PEG3350, 0.1M CaCl2, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 23, 2000
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 26030 / Num. obs: 24357 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044 / Net I/σ(I): 53.7
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.097 / % possible all: 81.2

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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
Starting model: PDB ENTRY 1LP8

1lp8


Resolution: 1.7→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2398 10 %RANDOM
Rwork0.19 ---
all0.195 24193 --
obs0.195 24002 --
Displacement parametersBiso mean: 16.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 22 175 2213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.145
X-RAY DIFFRACTIONx_improper_angle_d0.984

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