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- PDB-6obm: Ricin A chain bound to VHH antibody V6A7 -

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Basic information

Entry
Database: PDB / ID: 6obm
TitleRicin A chain bound to VHH antibody V6A7
Components
  • Ricin A chain
  • VHH antibody V6A7
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 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / 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 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / 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: 2.495 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 21, 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 V6A7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9123
Polymers41,8772
Non-polymers351
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint0 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.654, 102.654, 156.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Ricin A chain


Mass: 29015.645 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 V6A7


Mass: 12861.096 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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 200 mM potassium sulfate and 20% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.495→50 Å / Num. obs: 14935 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 58.61 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.029 / Rrim(I) all: 0.108 / Χ2: 1.012 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5471.5457110.480.5771.6590.64294.8
2.54-2.598.81.2556830.7340.4251.330.65599.1
2.59-2.6410.51.2077520.7860.3811.2680.66100
2.64-2.69131.2457400.8630.3561.2960.689100
2.69-2.7514.21.0627210.920.2921.1020.68100
2.75-2.8214.60.9367540.9370.2530.970.711100
2.82-2.8914.70.6987220.9430.1880.7230.734100
2.89-2.9614.70.5637480.980.1520.5830.759100
2.96-3.0514.60.4427430.9770.120.4590.768100
3.05-3.1514.60.3397440.9840.0920.3510.805100
3.15-3.2614.60.2717290.9910.0730.2810.828100
3.26-3.3914.60.1797340.9940.0480.1850.917100
3.39-3.5514.50.147630.9980.0380.1450.986100
3.55-3.7314.50.1027340.9980.0280.1061.078100
3.73-3.9714.30.0847580.9980.0230.0871.172100
3.97-4.2714.30.0677640.9990.0180.0691.338100
4.27-4.714.20.0617490.9980.0170.0631.674100
4.7-5.38140.0627680.9990.0170.0651.857100
5.38-6.7813.60.0577760.9990.0160.0591.574100
6.78-5012.90.0338420.9990.0090.0341.20499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.59 Å
Translation2.5 Å46.59 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.495→46.595 Å / SU ML: 0.73 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.2
RfactorNum. reflection% reflection
Rfree0.2606 671 4.49 %
Rwork0.2089 --
obs0.2113 14930 99.66 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 50.612 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 152.59 Å2 / Biso mean: 69.98 Å2 / Biso min: 35.12 Å2
Baniso -1Baniso -2Baniso -3
1-4.0531 Å20 Å2-0 Å2
2--4.0531 Å2-0 Å2
3----8.1061 Å2
Refinement stepCycle: final / Resolution: 2.495→46.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 1 14 2952
Biso mean--79.48 54.68 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032997
X-RAY DIFFRACTIONf_angle_d0.7324072
X-RAY DIFFRACTIONf_chiral_restr0.051451
X-RAY DIFFRACTIONf_plane_restr0.003537
X-RAY DIFFRACTIONf_dihedral_angle_d14.0871089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4954-2.6880.34481240.32362763288798
2.688-2.95850.31431320.290428132945100
2.9585-3.38650.32561180.238528312949100
3.3865-4.26620.21961710.191628463017100
4.2662-46.6030.25551260.17930063132100
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)
11.5283-1.6505-0.69916.29621.30195.4647-0.326-0.30220.16620.7520.3069-0.38110.49950.1860.03960.3764-0.0354-0.07490.4281-0.01780.4029-21.43126.95-16.386
25.0638-1.89891.26586.41020.8027.1113-0.3383-0.1930.09490.3120.05770.2705-0.2583-0.26450.17280.30220.02980.02670.3224-0.05610.2786-36.240912.6746-19.6913
33.2225-2.14581.17565.2202-1.55912.2552-0.10650.0909-0.1844-0.00220.1340.0572-0.00350.1608-0.0360.2773-0.02620.00520.3513-0.01650.2612-27.655-3.1087-26.8689
44.46352.10840.65324.4726-0.55576.08580.7491-0.4177-0.11640.7375-0.240.14181.0637-1.4987-0.29970.765-0.16320.36220.79280.07980.7712-48.3604-26.3759-21.0038
55.58811.19080.25379.33610.52121.18450.31260.19380.58130.535-0.44261.7490.2165-0.31470.11910.4834-0.16660.17290.652-0.14650.8443-47.4154-14.4855-21.4405
67.9716-1.9225-1.37012.1212-0.62187.8446-0.1624-1.7245-0.7271.1583-0.40440.69570.82420.22050.37010.9194-0.0658-0.01550.65970.0890.6062-36.1394-26.5806-20.2996
78.1107-1.815-0.17596.1812-3.55076.2980.06380.6369-0.32120.5017-0.35120.0930.74130.46820.16080.5207-0.0427-0.05230.4942-0.04410.3197-36.9435-19.4099-29.1964
89.0606-4.6638-5.53932.8633.95746.20680.27870.23271.1807-0.10470.3004-0.58360.2646-0.2653-0.48970.388-0.13120.04220.54360.0450.5331-46.3834-20.1361-29.7227
94.64745.29931.52776.1412.41944.18850.43690.1314-0.6773-0.1573-0.50940.47541.22250.2940.09440.89660.13810.05150.4166-0.03970.4402-40.3053-28.5694-24.1242
102.6313.1291-0.67257.7375-1.09821.71020.4615-0.980.09591.6959-0.74411.54530.6866-0.16390.28670.8697-0.12830.14820.57990.04680.6154-39.7321-16.7236-17.6501
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 1:18)B1 - 18
5X-RAY DIFFRACTION5chain 'B' and (resseq 19:34)B19 - 34
6X-RAY DIFFRACTION6chain 'B' and (resseq 35:45)B35 - 45
7X-RAY DIFFRACTION7chain 'B' and (resseq 46:64)B46 - 64
8X-RAY DIFFRACTION8chain 'B' and (resseq 65:83)B65 - 83
9X-RAY DIFFRACTION9chain 'B' and (resseq 84:100)B84 - 100
10X-RAY DIFFRACTION10chain 'B' and (resseq 101:120)B101 - 120

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