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- PDB-3hiw: Crystal structure of Saporin-L1 in complex with the cyclic tetran... -

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Basic information

Entry
Database: PDB / ID: 3hiw
TitleCrystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue
ComponentsVacuolar saporin
KeywordsHydrolase/Hydrolase inhibitor / transition state / ribosome inactivating proteins / RIPs / Hydrolase / Plant defense / Protein synthesis inhibitor / Toxin / Hydrolase-Hydrolase inhibitor COMPLEX
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
Chem-C2X / rRNA N-glycosylase
Similarity search - Component
Biological speciesSaponaria officinalis (common soapwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7324
Polymers57,5362
Non-polymers3,1962
Water7,963442
1
A: Vacuolar saporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3662
Polymers28,7681
Non-polymers1,5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vacuolar saporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3662
Polymers28,7681
Non-polymers1,5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.555, 52.573, 54.369
Angle α, β, γ (deg.)78.870, 66.320, 80.580
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
#2: Chemical ChemComp-C2X / 9,9'-{(2R,3R,3aR,5S,7aR,9R,10R,10aR,12S,23R,25aR,27R,28R,28aR,30S,32aR,35aR,37S,39aR)-9-(6-amino-9H-purin-9-yl)-34-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-5,12,23,30,37-pentahydroxy-3,10,28-trimethoxy-5,12,23,30,37-pentaoxidotetracosahydro-2H,7H,25H-trifuro[3,2-f:3',2'-l:3'',2''-x]pyrrolo[3,4-r][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]undecaoxazapentaphosphacyclopentatriacontine-2,27-diyl}bis(2-amino-3,9-dihydro-6H-purin-6-one)


Mass: 1598.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H72N21O29P5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
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: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 44853 / % possible obs: 97.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.041 / Χ2: 1.031 / Net I/σ(I): 18.983
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.861.90.21644090.88695.6
1.86-1.9420.1744591.04295.8
1.94-2.0320.11344290.97896.4
2.03-2.1320.09344441.09496.4
2.13-2.271.90.07344771.04996.6
2.27-2.441.90.05744861.00297.5
2.44-2.691.90.04645101.05197.7
2.69-3.071.90.03545361.11597.8
3.07-3.871.90.02545521.03398.3
3.87-2020.02345511.05198.6

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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: 1.8→19.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.65 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2276 5.1 %RANDOM
Rwork0.181 ---
obs0.184 44846 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.23 Å2 / Biso mean: 17.906 Å2 / Biso min: 7.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.02 Å2-0.05 Å2
2---0.07 Å20.06 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 212 442 4684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224393
X-RAY DIFFRACTIONr_angle_refined_deg1.3252.0226021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2165530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20425.155194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13115715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4151522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213244
X-RAY DIFFRACTIONr_mcbond_it0.6191.52581
X-RAY DIFFRACTIONr_mcangle_it1.11724190
X-RAY DIFFRACTIONr_scbond_it1.80631812
X-RAY DIFFRACTIONr_scangle_it3.0814.51822
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 149 -
Rwork0.227 2987 -
all-3136 -
obs--93.42 %

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