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- PDB-6cwk: Anti-RTA VHH antibody -

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Basic information

Entry
Database: PDB / ID: 6cwk
TitleAnti-RTA VHH antibody
ComponentsAnti-Ricin antibody
KeywordsIMMUNE SYSTEM / Ricin binding antibody
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.256 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: Protein Eng. Des. Sel. / Year: 2018
Title: Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity.
Authors: Rudolph, M.J. / Vance, D.J. / Kelow, S. / Angalakurthi, S.K. / Nguyen, S. / Davis, S.A. / Rong, Y. / Middaugh, C.R. / Weis, D.D. / Dunbrack Jr., R. / Karanicolas, J. / Mantis, N.J.
History
DepositionMar 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-Ricin antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1047
Polymers14,7161
Non-polymers3876
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-36 kcal/mol
Surface area6600 Å2
Unit cell
Length a, b, c (Å)60.294, 60.294, 81.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-43-

LYS

21A-332-

HOH

31A-425-

HOH

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Components

#1: Antibody Anti-Ricin antibody


Mass: 14716.448 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)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 200 mM NaCl, 100 mM Na Acetate, 1.7 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.256→50 Å / Num. obs: 41576 / % possible obs: 99.7 % / Redundancy: 7 % / Net I/σ(I): 57.8
Reflection shellResolution: 1.26→1.28 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.256→37.766 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.49
RfactorNum. reflection% reflection
Rfree0.1755 2034 4.91 %
Rwork0.1552 --
obs0.1562 41400 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122 Å2 / Biso mean: 27.5411 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.256→37.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 20 141 1125
Biso mean--58.28 39.42 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231179
X-RAY DIFFRACTIONf_angle_d1.8621613
X-RAY DIFFRACTIONf_chiral_restr0.113164
X-RAY DIFFRACTIONf_plane_restr0.013214
X-RAY DIFFRACTIONf_dihedral_angle_d16.286440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2556-1.28480.25881080.25942458256694
1.2848-1.31690.22731270.230425942721100
1.3169-1.35260.22371330.218825932726100
1.3526-1.39240.2151450.207125932738100
1.3924-1.43730.21651420.194726022744100
1.4373-1.48870.22491460.197125872733100
1.4887-1.54830.22271290.187726192748100
1.5483-1.61870.18591300.169726022732100
1.6187-1.70410.19311230.172226412764100
1.7041-1.81090.17311280.16526402768100
1.8109-1.95070.16131470.154826342781100
1.9507-2.1470.14541440.141726432787100
2.147-2.45760.15981370.137426722809100
2.4576-3.09610.16961440.143227092853100
3.0961-37.78350.17071510.13932779293097
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)
19.4376-6.81324.90334.9928-4.90076.9907-0.0746-0.6084-0.50780.19650.28270.36160.1789-0.0802-0.26590.1589-0.01810.00360.22680.02730.227319.864910.071221.2216
22.81771.29690.48978.1277-1.62883.6766-0.2167-0.26510.54080.2062-0.0083-0.1002-0.3972-0.35130.2170.13090.0586-0.00170.1974-0.04220.165916.733723.643516.9603
34.4521-1.14853.26651.4572-0.81885.6510.071-0.3715-0.30620.11340.13230.02020.3064-0.1938-0.17390.1018-0.0171-0.01490.09760.01790.11629.223911.188122.6168
47.96482.94447.05263.79432.53285.8409-0.27810.50710.0494-0.51430.20590.0143-0.24780.30270.11420.1404-0.0288-0.01120.1349-0.00190.096626.208615.80867.186
57.0395-1.78751.44496.4993-2.07122.7348-0.13260.3060.3142-0.20790.0135-0.1289-0.0620.07970.14550.1048-0.0272-0.02580.0921-0.02390.103232.122521.73218.9804
65.1922-3.60883.39947.6879-5.93244.6008-0.1764-0.51970.06950.28520.25660.2543-0.126-0.5585-0.10810.18230.0238-0.01810.2116-0.03370.140423.365119.117824.0755
76.9254.07684.31042.42892.53862.664-0.46310.24230.4613-0.31660.2976-0.2108-0.69020.27960.00560.2471-0.0371-0.06780.1510.02620.245820.583327.52977.6419
86.0297-0.73332.89780.9175-1.2162.77690.0180.0048-0.2081-0.09830.0063-0.05480.12530.0559-0.02660.12240.0076-0.00450.088-0.02910.107732.35311.808915.9856
97.7371-3.98632.49757.8166-3.29813.5362-0.0556-0.0307-0.3416-0.08490.07560.14030.037-0.0419-0.05120.104-0.0371-0.02330.0923-0.04040.05221.956912.49112.8413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 23 )A11 - 23
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 39 )A24 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 51 )A40 - 51
5X-RAY DIFFRACTION5chain 'A' and (resid 52 through 75 )A52 - 75
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 85 )A76 - 85
7X-RAY DIFFRACTION7chain 'A' and (resid 86 through 93 )A86 - 93
8X-RAY DIFFRACTION8chain 'A' and (resid 94 through 112 )A94 - 112
9X-RAY DIFFRACTION9chain 'A' and (resid 113 through 129 )A113 - 129

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