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- PDB-3his: Crystal structure of Saporin-L1 from Saponaria officinalis -

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Basic information

Entry
Database: PDB / ID: 3his
TitleCrystal structure of Saporin-L1 from Saponaria officinalis
ComponentsVacuolar saporin
KeywordsHYDROLASE / transition state analogue / ribosome inactivating proteins / RIPs / Plant defense / Protein synthesis inhibitor / Toxin
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
Biological speciesSaponaria officinalis (common soapwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHo, M. / Sturm, M.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
Authors: Ho, M.C. / Sturm, M.B. / Almo, S.C. / Schramm, V.L.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar saporin
B: Vacuolar saporin


Theoretical massNumber of molelcules
Total (without water)57,5362
Polymers57,5362
Non-polymers00
Water8,485471
1
A: Vacuolar saporin


Theoretical massNumber of molelcules
Total (without water)28,7681
Polymers28,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vacuolar saporin


Theoretical massNumber of molelcules
Total (without water)28,7681
Polymers28,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.939, 53.058, 54.632
Angle α, β, γ (deg.)78.860, 65.620, 80.650
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Vacuolar saporin


Mass: 28767.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saponaria officinalis (common soapwort)
Production host: Escherichia coli (E. coli) / References: UniProt: Q2QEH4, rRNA N-glycosylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG2000MME, 0.1M sodium acetate, 0.4M potassium thiocyanate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.49→51.85 Å / Num. obs: 76910 / % possible obs: 92.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.069 / Χ2: 1.041 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.49-1.542.60.51778351.07294.3
1.54-1.612.60.37979001.05594.9
1.61-1.682.60.30578651.04895.2
1.68-1.772.60.22680311.0595.8
1.77-1.882.60.16779541.00796.2
1.88-2.022.40.11176870.98792.4
2.02-2.232.60.0757400188.9
2.23-2.552.40.05667911.05181.8
2.55-3.212.60.04281891.03598.3
3.21-502.50.0372581.187.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.367 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3842 5 %RANDOM
Rwork0.208 ---
obs0.21 76828 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.5 Å2 / Biso mean: 12.985 Å2 / Biso min: 5.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0.18 Å2-0.28 Å2
2---0.16 Å20.5 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 0 471 4501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224193
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9615721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44925.13193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3615717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2761522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213196
X-RAY DIFFRACTIONr_mcbond_it0.5891.52614
X-RAY DIFFRACTIONr_mcangle_it1.03324251
X-RAY DIFFRACTIONr_scbond_it1.80931579
X-RAY DIFFRACTIONr_scangle_it2.9884.51466
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 260 -
Rwork0.29 5499 -
all-5759 -
obs--93.34 %

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