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- PDB-2g5x: Crystal structure of lychnin a type 1 Ribosome Inactivating Prote... -

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Basic information

Entry
Database: PDB / ID: 2g5x
TitleCrystal structure of lychnin a type 1 Ribosome Inactivating Protein (RIP)
ComponentsRibosome-inactivating protein
KeywordsHYDROLASE / alpha-beta protein
Function / homologyRicin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesLychnis chalcedonica (scarlet lychnis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFermani, S. / Falini, G. / Tosi, G. / Ripamonti, A. / Polito, L. / Bolognesi, A. / Stirpe, F.
Citation
Journal: To be Published
Title: Crystal structure of lychnin a type 1 Ribosome Inactivating Protein (RIP)
Authors: Fermani, S. / Falini, G. / Tosi, G. / Ripamonti, A. / Polito, L. / Bolognesi, A. / Stirpe, F.
#1: Journal: Biochim.Biophys.Acta / Year: 1990
Title: Purification and properties of new ribosome-inactivating proteins with RNA N-glycosidase activity
Authors: Bolognesi, A. / Barbieri, L. / Abbondanza, A. / Falasca, A.I. / Carnicelli, D. / Battelli, M.G. / Stirpe, F.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray diffraction analysis of two ribosome-inactivating proteins: lychnin and dianthin 30
Authors: Fermani, S. / Falini, G. / Ripamonti, A. / Bolognesi, A. / Polito, L. / Stirpe, F.
History
DepositionFeb 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome-inactivating protein


Theoretical massNumber of molelcules
Total (without water)26,1641
Polymers26,1641
Non-polymers00
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.247, 57.333, 53.230
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe protein is a monomer. The asymmetric unit contain one monomer

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Components

#1: Protein Ribosome-inactivating protein / LYCHNIN


Mass: 26163.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lychnis chalcedonica (scarlet lychnis) / Tissue: seeds / References: rRNA N-glycosylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 8000, 0.1M sodium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 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: 1.7→29.1 Å / Num. all: 22021 / Num. obs: 21895 / % possible obs: 51 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.048 / Net I/σ(I): 39.7
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 14.2 / Num. unique all: 2162 / Rsym value: 0.084 / % possible all: 50.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WUC

1wuc
PDB Unreleased entry


Resolution: 1.7→28.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 948638.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2170 9.9 %RANDOM
Rwork0.162 ---
all0.164 22502 --
obs0.162 21878 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.4733 Å2 / ksol: 0.460368 e/Å3
Displacement parametersBiso mean: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-1.14 Å2
2---0.5 Å20 Å2
3----1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 0 364 2227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.352
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 305 9.6 %
Rwork0.192 2875 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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