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- PDB-1rl0: Crystal structure of a new ribosome-inactivating protein (RIP): d... -

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Basic information

Entry
Database: PDB / ID: 1rl0
TitleCrystal structure of a new ribosome-inactivating protein (RIP): dianthin 30
ComponentsAntiviral protein DAP-30
KeywordsHYDROLASE / PLANT PROTEIN / mixed beta-sheet / alpha and beta regions
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
Ribosome-inactivating protein dianthin-30
Similarity search - Component
Biological speciesDianthus caryophyllus (clove pink)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFermani, S. / Falini, G. / Ripamonti, A. / Bolognesi, A. / Polito, L. / Stirpe, F.
Citation
Journal: J.Struct.Biol. / Year: 2005
Title: The 1.4A structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins
Authors: Fermani, S. / Falini, G. / Ripamonti, A. / Polito, L. / Stirpe, F. / Bolognesi, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary X-ray diffraction analysis of two ribosomes-inactivating proteins: lychnin and dianthin 30
Authors: Fermani, S. / Falini, G. / Ripamonti, A. / Bolognesi, A. / Polito, L. / Stirpe, F.
#2: Journal: Biochim.Biophys.Acta / Year: 1993
Title: Ribosome-inactivating proteins from plants
Authors: Barbieri, L. / Battelli, M.G. / Stirpe, F.
#3: Journal: Biochem.J. / Year: 1981
Title: Dianthins, ribosome-damaging proteins with anti-viral properties from Dianthus caryophyllus L. (carnation)
Authors: Stirpe, F. / Williams, D.G. / Onyon, L.G. / Legg, R.F. / Stevens, W.A.
History
DepositionNov 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antiviral protein DAP-30


Theoretical massNumber of molelcules
Total (without water)28,6331
Polymers28,6331
Non-polymers00
Water8,773487
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.568, 78.654, 43.136
Angle α, β, γ (deg.)90.00, 105.39, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe protein is a monomeric enzyme, the asymmetric unit contains a single chain.

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Components

#1: Protein Antiviral protein DAP-30 / E.C.3.2.2.22 / Ribosome-inactivating protein / rRNA N-glycosidase


Mass: 28632.631 Da / Num. of mol.: 1 / Fragment: residues 24-278 / Source method: isolated from a natural source / Source: (natural) Dianthus caryophyllus (clove pink) / Organ: leaves / References: UniProt: P24476, rRNA N-glycosylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 1.72 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 293 K / pH: 4.5
Details: PEG 4000, ammonium acetate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2002 / Details: mirrors
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→39 Å / Num. obs: 44547 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.063 / Net I/σ(I): 26.3
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 10.4 / Rsym value: 0.255 / % possible all: 90.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1QI7

1qi7


Resolution: 1.4→36.22 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 916080.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2235 5 %RANDOM
Rwork0.184 ---
all0.1841 44520 --
obs0.1841 44520 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.95 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å2-1.8 Å2
2--3.26 Å20 Å2
3----1.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.4→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 0 487 2550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 342 4.8 %
Rwork0.225 6749 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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