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- PDB-1qi7: THE CRYSTAL STRUCTURE AT 2.0 A OF SAPORIN SO6, A RIBOSOME INACTIV... -

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Basic information

Entry
Database: PDB / ID: 1qi7
TitleTHE CRYSTAL STRUCTURE AT 2.0 A OF SAPORIN SO6, A RIBOSOME INACTIVATING PROTEIN FROM SAPONARIA OFFICINALIS
ComponentsPROTEIN (N-GLYCOSIDASE)
KeywordsHYDROLASE / RIBOSOME INACTIVATING PROTEIN / N-GLYCOSIDASE
Function / homology
Function and homology information


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 saporin-6 / Ribosome-inactivating protein saporin-2
Similarity search - Component
Biological speciesSaponaria officinalis (common soapwort)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSavino, C. / Federici, L. / Ippoliti, R. / Lendaro, E. / Tsernoglou, D.
CitationJournal: FEBS Lett. / Year: 2000
Title: The crystal structure of saporin SO6 from Saponaria officinalis and its interaction with the ribosome.
Authors: Savino, C. / Federici, L. / Ippoliti, R. / Lendaro, E. / Tsernoglou, D.
History
DepositionJun 8, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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: PROTEIN (N-GLYCOSIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7212
Polymers28,6251
Non-polymers961
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (N-GLYCOSIDASE)
hetero molecules

A: PROTEIN (N-GLYCOSIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4424
Polymers57,2492
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Buried area1990 Å2
ΔGint-49 kcal/mol
Surface area21580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.530, 67.530, 119.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein PROTEIN (N-GLYCOSIDASE)


Mass: 28624.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saponaria officinalis (common soapwort) / Cellular location: CYTOPLASM / Organ: SEEDS
References: UniProt: P27559, UniProt: P20656*PLUS, rRNA N-glycosylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growpH: 4.7 / Details: pH 4.7
Crystal grow
*PLUS
Temperature: 309 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
310 %(w/v)PEG4001drop
42.8 Mammonium sulfate1reservoir
50.1 Msodium citrate1reservoir
2reservoir solution1drop

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Data collection

DiffractionMean temperature: 309 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 19206 / % possible obs: 98.5 % / Redundancy: 8.7 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.101
Reflection shellResolution: 2→2.23 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.294 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 210203 / Rmerge(I) obs: 0.109
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PAF

1paf


Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -5 %RANDOM
Rwork0.182 ---
obs-19206 98.5 %-
Displacement parametersBiso mean: 22.6 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 5 113 2135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d2.24
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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