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- PDB-3hiv: Crystal structure of Saporin-L1 in complex with the trinucleotide... -

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Basic information

Entry
Database: PDB / ID: 3hiv
TitleCrystal structure of Saporin-L1 in complex with the trinucleotide 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-TXN / rRNA N-glycosylase
Similarity search - Component
Biological speciesSaponaria officinalis (common soapwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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: Refinement description / 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)59,7754
Polymers57,5362
Non-polymers2,2402
Water1,65792
1
A: Vacuolar saporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8882
Polymers28,7681
Non-polymers1,1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vacuolar saporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8882
Polymers28,7681
Non-polymers1,1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.329, 52.884, 54.239
Angle α, β, γ (deg.)79.41, 66.46, 80.67
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: Chemical ChemComp-TXN / (2R,3R,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-amino-6-oxo-6,8-dihydro-9H-purin-9-yl)-2-(hydroxymethyl)-4-methoxytetrahydrofuran-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]pyrrolidin-3-yl}oxy)(hydroxy)phosphoryl]oxy}methyl)-4-methoxytetrahydrofuran-3-yl 3-hydroxypropyl hydrogen (S)-phosphate


Mass: 1119.819 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H52N15O20P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 45.34 %
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: 1.081 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 2.14→51.71 Å / Num. obs: 25749 / % possible obs: 93.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.573
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.14-2.232.10.357172.2
2.23-2.322.20.337184.5
2.32-2.422.50.296192.5
2.42-2.552.80.276196.2
2.55-2.713.10.23197.2
2.71-2.923.10.155197.9
2.92-3.213.20.095197.9
3.21-3.673.10.065198.4
3.67-4.6130.046198.2
4.61-203.30.038199.2

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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: 2.14→51.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.545 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22879 1297 5 %RANDOM
Rwork0.18923 ---
obs0.19136 24447 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.539 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å21.88 Å2-1.67 Å2
2---1.54 Å2-1.87 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.14→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 150 92 4272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224277
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6252.0055839
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.47225.079191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58915702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9921522
X-RAY DIFFRACTIONr_chiral_restr0.1040.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213174
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5531.52557
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01724140
X-RAY DIFFRACTIONr_scbond_it1.82931720
X-RAY DIFFRACTIONr_scangle_it3.0264.51698
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.191 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 56 -
Rwork0.25 1208 -
obs--60.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.07710.43450.60050.91550.07950.9292-0.0378-0.01510.00990.0232-0.0458-0.1046-0.0136-0.02190.08370.17980.01030.00190.16290.01040.113831.50758.97249.565
20.39610.22040.48452.18310.7361.3020.00690.05960.01480.03180.0611-0.30890.04020.0949-0.06810.127-0.01220.03060.1450.02490.173526.32130.91424.61
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 257
2X-RAY DIFFRACTION2B35 - 257

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