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- PDB-5sv4: Anti-Ricin A-chain Single Domain Antibody A3C8 -

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Basic information

Entry
Database: PDB / ID: 5sv4
TitleAnti-Ricin A-chain Single Domain Antibody A3C8
ComponentsSingle Domain Antibody A3C8
KeywordsTOXIN / single domain antibody / sdAb / ricin / A-chain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single Domain Antibody A3C8
B: Single Domain Antibody A3C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3534
Polymers30,1612
Non-polymers1922
Water1,08160
1
A: Single Domain Antibody A3C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2733
Polymers15,0811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Single Domain Antibody A3C8


Theoretical massNumber of molelcules
Total (without water)15,0811
Polymers15,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Single Domain Antibody A3C8
hetero molecules

B: Single Domain Antibody A3C8


Theoretical massNumber of molelcules
Total (without water)30,3534
Polymers30,1612
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Buried area1010 Å2
ΔGint-37 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.883, 44.395, 143.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Single Domain Antibody 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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 35.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Citric acid pH 5.0, 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: Oct 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→47.92 Å / Num. obs: 6826 / % possible obs: 100 % / Redundancy: 11.52 % / Rsym value: 0.1663 / Net I/σ(I): 12.24
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.15 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.47 / % 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: 4fhb

4fhb


Resolution: 2.7→47.92 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24595 327 4.8 %RANDOM
Rwork0.19827 ---
obs0.20056 6455 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.034 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.39 Å2-0 Å2
3----1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 10 60 1990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191964
X-RAY DIFFRACTIONr_bond_other_d00.021782
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.942670
X-RAY DIFFRACTIONr_angle_other_deg3.91834082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13823.40988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65815300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.631516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022280
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02468
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_it1.4152.6571014
X-RAY DIFFRACTIONr_mcbond_other1.4152.6551013
X-RAY DIFFRACTIONr_mcangle_it2.483.9771264
X-RAY DIFFRACTIONr_mcangle_other2.4793.9791265
X-RAY DIFFRACTIONr_scbond_it1.3352.839950
X-RAY DIFFRACTIONr_scbond_other1.3152.816943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3454.171395
X-RAY DIFFRACTIONr_long_range_B_refined4.77420.8722155
X-RAY DIFFRACTIONr_long_range_B_other4.7320.912146
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 13 -
Rwork0.26 496 -
obs--100 %

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