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- PDB-5sv3: RTA1-33/44-198 (RVEC) bound to Single Domain Antibody A3C8 -

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Basic information

Entry
Database: PDB / ID: 5sv3
TitleRTA1-33/44-198 (RVEC) bound to Single Domain Antibody A3C8
Components
  • Anti-Ricin A-chain Single Domain Antibody (sdAb) A3C8
  • Ricin
KeywordsTOXIN / Ricin / A-chain / RVEC / sdAb / antibody / RTA1-33/44-198
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 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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Ricinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsCompton, J.R. / Legler, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)CBCALL12-LS6-2-0036 United States
CitationJournal: MAbs / Year: 2017
Title: Stability of isolated antibody-antigen complexes as a predictive tool for selecting toxin neutralizing antibodies.
Authors: Legler, P.M. / Compton, J.R. / Hale, M.L. / Anderson, G.P. / Olson, M.A. / Millard, C.B. / Goldman, E.R.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-Ricin A-chain Single Domain Antibody (sdAb) A3C8
B: Ricin
C: Anti-Ricin A-chain Single Domain Antibody (sdAb) A3C8
D: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4306
Polymers73,2384
Non-polymers1922
Water1,40578
1
A: Anti-Ricin A-chain Single Domain Antibody (sdAb) A3C8
B: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7153
Polymers36,6192
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Anti-Ricin A-chain Single Domain Antibody (sdAb) A3C8
D: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7153
Polymers36,6192
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.759, 130.432, 35.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody Anti-Ricin A-chain Single Domain Antibody (sdAb) A3C8


Mass: 15080.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Ricin /


Mass: 21538.275 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.9 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 1.6 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.73→65.22 Å / Num. obs: 15475 / % possible obs: 99.9 % / Redundancy: 13.97 % / Rsym value: 0.1871 / Net I/σ(I): 11.91
Reflection shellResolution: 2.73→2.83 Å / Redundancy: 14.19 % / Rmerge(I) obs: 0.4543 / Mean I/σ(I) obs: 4.52 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LC9

3lc9


Resolution: 2.73→65.22 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.868 / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 783 5.1 %RANDOM
Rwork0.22634 ---
obs0.22838 14603 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.777 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2---2.2 Å20 Å2
3---2.31 Å2
Refinement stepCycle: 1 / Resolution: 2.73→65.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 10 78 4623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194633
X-RAY DIFFRACTIONr_bond_other_d00.024278
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9426302
X-RAY DIFFRACTIONr_angle_other_deg3.83139755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1365579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10523.48227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55815704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9851538
X-RAY DIFFRACTIONr_chiral_restr0.0620.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025395
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021159
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_it1.2182.632334
X-RAY DIFFRACTIONr_mcbond_other1.2182.6292333
X-RAY DIFFRACTIONr_mcangle_it2.2693.9332907
X-RAY DIFFRACTIONr_mcangle_other2.2693.9352908
X-RAY DIFFRACTIONr_scbond_it0.8272.7072299
X-RAY DIFFRACTIONr_scbond_other0.8272.72292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6334.0023384
X-RAY DIFFRACTIONr_long_range_B_refined3.71520.3254944
X-RAY DIFFRACTIONr_long_range_B_other3.71520.3224939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.73→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 51 -
Rwork0.285 1077 -
obs--99.82 %

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