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- PDB-6obc: Ricin A chain bound to camelid -

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Basic information

Entry
Database: PDB / ID: 6obc
TitleRicin A chain bound to camelid
Components
  • Ricin A chain
  • VHH antibody
KeywordsTOXIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / 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 / Ricin-type beta-trefoil lectin domain / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / 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 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.762 Å
AuthorsRudolph, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site.
Authors: Rudolph, M.J. / Czajka, T.F. / Davis, S.A. / Thi Nguyen, C.M. / Li, X.P. / Tumer, N.E. / Vance, D.J. / Mantis, N.J.
History
DepositionMar 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
B: VHH antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4168
Polymers42,1232
Non-polymers2936
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-24 kcal/mol
Surface area16580 Å2
Unit cell
Length a, b, c (Å)38.748, 47.197, 58.430
Angle α, β, γ (deg.)100.250, 97.300, 109.710
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ricin A chain


Mass: 29000.676 Da / Num. of mol.: 1 / Fragment: Toxin catalytic subunit, residues 40-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody VHH antibody


Mass: 13122.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 100 mM Tris (pH 7.0), 200 mM calcium acetate, and 20% PEG 3,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 35851 / % possible obs: 96.8 % / Redundancy: 2 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Rrim(I) all: 0.096 / Χ2: 0.794 / Net I/σ(I): 6 / Num. measured all: 70534
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.7920.64617170.6470.6460.9140.62396.4
1.79-1.8220.63818090.7030.6380.9020.62895.5
1.82-1.8620.57517490.7220.5750.8140.66895
1.86-1.920.46118080.790.4610.6510.65996.1
1.9-1.9420.37417590.840.3740.5280.71294.9
1.94-1.9820.30417630.8840.3040.430.73596.5
1.98-2.0320.2517870.9180.250.3540.73295.9
2.03-2.0920.20917850.9470.2090.2960.78797.1
2.09-2.1520.17618100.9540.1760.2490.77696.1
2.15-2.2220.15817690.9640.1580.2240.84597.4
2.22-2.320.13517900.970.1350.190.81796
2.3-2.3920.12118120.9750.1210.1720.80197.4
2.39-2.520.11117800.9780.1110.1570.80397.2
2.5-2.6320.09218410.9870.0920.130.8897
2.63-2.7920.07417830.9890.0740.1040.83397
2.79-3.0120.06117740.9920.0610.0860.94597.2
3.01-3.3120.04418480.9940.0440.0620.94298
3.31-3.791.90.03117940.9970.0310.0430.92197.6
3.79-4.781.90.02218260.9980.0220.0310.83298.4
4.78-5020.02418470.9970.0240.0350.93999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å43.17 Å
Translation2 Å43.17 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX(1.7.1_743)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.762→43.173 Å / FOM work R set: 0.7945 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1736 4.85 %
Rwork0.1851 34080 -
obs0.1872 35816 96.52 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.999 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 101.68 Å2 / Biso mean: 29.83 Å2 / Biso min: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.2226 Å22.426 Å2-2.9032 Å2
2--11.6957 Å2-10.6507 Å2
3----4.4731 Å2
Refinement stepCycle: final / Resolution: 1.762→43.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 15 272 3255
Biso mean--39.45 37.57 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063054
X-RAY DIFFRACTIONf_angle_d0.9734149
X-RAY DIFFRACTIONf_chiral_restr0.067455
X-RAY DIFFRACTIONf_plane_restr0.005549
X-RAY DIFFRACTIONf_dihedral_angle_d13.4411117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7619-1.81370.37011420.30822730287294
1.8137-1.87220.31391400.28442791293195
1.8722-1.93920.3241520.24822837298995
1.9392-2.01680.26331450.22942809295496
2.0168-2.10860.24471650.20732814297996
2.1086-2.21970.25791270.18752844297197
2.2197-2.35880.25381190.17952894301397
2.3588-2.54090.21691460.17662873301997
2.5409-2.79660.21771460.17982839298597
2.7966-3.20110.22111370.17092870300797
3.2011-4.03260.19621460.15672864301098
4.0326-43.18570.18881710.16312915308699
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)
10.61260.39940.28510.44470.1270.772-0.0407-0.17010.2116-0.0306-0.04450.0734-0.068-0.05350.08560.19260.03940.00320.25-0.02850.2564-3.215815.502332.762
22.9577-0.06980.34272.3298-1.0133.41950.04480.05470.2212-0.01340.0189-0.0953-0.31520.1508-0.07270.1580.0150.00510.1533-0.03930.207112.909717.323633.9398
32.82530.5271.06060.9240.68292.11030.0512-0.061-0.13660.0887-0.0250.0340.1616-0.0814-0.03430.15680.01040.01790.12750.0030.15932.34820.949932.0403
42.2491.21720.86093.41082.3284.5302-0.04360.11730.1302-0.15490.0877-0.0477-0.10970.0352-0.04880.14810.0331-0.00490.2535-0.0130.177310.6168-10.80438.4465
54.06050.15245.21080.9050.7067.118-0.2188-0.06650.333-0.1009-0.53490.4477-0.224-1.09270.6410.21750.0561-0.01410.4875-0.14590.28521.0381-12.856713.248
66.22984.96941.81716.4548-1.52154.0760.6238-1.30430.61171.7018-0.3663-0.2406-0.3056-0.2336-0.21490.4229-0.0048-0.05050.5861-0.17910.346111.7726-13.296623.4845
76.13543.97840.62937.04260.55617.87110.7724-1.1061-0.29560.7838-0.73070.25150.6487-0.4128-0.09420.3275-0.0053-0.00780.37270.00040.30979.1744-20.046915.3854
81.41550.15811.00124.06883.3534.58570.1220.1579-0.15210.01390.0283-0.13550.14180.112-0.0940.1683-0.0081-0.00160.2241-0.00530.14758.9727-13.202810.3646
91.24442.00791.62777.89496.387.1346-0.11730.1449-0.0106-0.6724-0.04680.1443-0.3991-0.10510.10620.22250.017-0.02310.18640.01590.18955.2805-6.65688.8367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:56)A5 - 56
2X-RAY DIFFRACTION2chain 'A' and (resseq 57:122)A57 - 122
3X-RAY DIFFRACTION3chain 'A' and (resseq 123:263)A123 - 263
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:40)B1 - 40
5X-RAY DIFFRACTION5chain 'B' and (resseq 41:52)B41 - 52
6X-RAY DIFFRACTION6chain 'B' and (resseq 53:59)B53 - 59
7X-RAY DIFFRACTION7chain 'B' and (resseq 60:72)B60 - 72
8X-RAY DIFFRACTION8chain 'B' and (resseq 73:101)B73 - 101
9X-RAY DIFFRACTION9chain 'B' and (resseq 102:119)B102 - 119

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