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- PDB-6dyx: Structure of VHH R419 isolated from a pre-immune phage display library -

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Basic information

Entry
Database: PDB / ID: 6dyx
TitleStructure of VHH R419 isolated from a pre-immune phage display library
ComponentsVHH R419
KeywordsIMMUNE SYSTEM / Nanobody VHH single domain antibody
Function / homologyACETATE ION
Function and homology information
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrooks, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SC3GM112532 United States
CitationJournal: BMC Res Notes / Year: 2019
Title: Structure of a VHH isolated from a naive phage display library.
Authors: White, B. / Huh, I. / Brooks, C.L.
History
DepositionJul 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
D: VHH R419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7914
Polymers13,5401
Non-polymers2513
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.281, 58.281, 155.358
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11D-378-

HOH

21D-432-

HOH

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Components

#1: Antibody VHH R419


Mass: 13539.957 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) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M ammonium sulfate 0.1 M MES 30% PEG MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→36.145 Å / Num. obs: 25716 / % possible obs: 99.2 % / Redundancy: 10.1 % / Biso Wilson estimate: 19.66 Å2 / Rpim(I) all: 0.067 / Rrim(I) all: 0.218 / Rsym value: 0.207 / Net I/av σ(I): 1.3 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.5-1.547.10.335216960.1260.3590.33591.5
1.54-1.588.30.2992.217960.1050.3180.29999.3
1.58-1.6310.50.2822.317730.0910.2970.28299.9
1.63-1.6810.70.2562.517180.0820.2690.256100
1.68-1.7310.60.2382.616760.0760.250.238100
1.73-1.7910.70.2192.716290.070.230.219100
1.79-1.8610.60.2152.615730.0680.2260.215100
1.86-1.9410.70.2072.715290.0670.2180.207100
1.94-2.0210.60.2142.614650.0680.2250.214100
2.02-2.1210.60.2162.613940.0690.2270.216100
2.12-2.2410.60.2112.613570.0670.2220.211100
2.24-2.3710.60.1992.612550.0640.210.199100
2.37-2.5410.60.1992.812160.0620.2080.199100
2.54-2.7410.50.2032.711190.0640.2130.203100
2.74-310.40.2092.710500.0660.2190.209100
3-3.3510.40.2022.79500.0650.2120.20299.9
3.35-3.8710.20.2032.68570.0650.2140.20399.7
3.87-4.749.70.2062.77240.0680.2170.20699
4.74-6.719.40.2052.65900.0690.2170.20599
6.71-36.1458.10.2232.53490.0840.240.22395.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DBA

6dba


Resolution: 1.5→36.145 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 1310 5.1 %
Rwork0.176 --
obs0.1767 25678 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→36.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 14 141 1008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007896
X-RAY DIFFRACTIONf_angle_d0.8751224
X-RAY DIFFRACTIONf_dihedral_angle_d7.719508
X-RAY DIFFRACTIONf_chiral_restr0.053131
X-RAY DIFFRACTIONf_plane_restr0.006157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56010.19771430.18542455X-RAY DIFFRACTION93
1.5601-1.63110.20081400.17612669X-RAY DIFFRACTION100
1.6311-1.71710.19171470.17172676X-RAY DIFFRACTION100
1.7171-1.82460.18071470.1722682X-RAY DIFFRACTION100
1.8246-1.96550.18261430.16552685X-RAY DIFFRACTION100
1.9655-2.16330.18341430.15872724X-RAY DIFFRACTION100
2.1633-2.47620.18061400.16092741X-RAY DIFFRACTION100
2.4762-3.11950.1811640.17522775X-RAY DIFFRACTION100
3.1195-36.15540.20291430.18862961X-RAY DIFFRACTION98
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)
14.16124.7154.64695.79315.99168.53930.3967-0.14160.3834-0.092-0.59980.4622-0.2603-1.30950.29120.20630.040.02150.32810.02860.23026.7933-10.5569-16.5418
22.76752.05611.81161.52751.38144.60930.19750.01570.06940.61450.10960-0.91850.065-0.26730.4248-0.01990.05780.1422-0.01430.351422.51414.6219-14.2692
38.01386.99212.71347.42373.64557.19420.00150.08840.21480.31110.2320.198-0.5581-0.1892-0.18170.26740.05240.03720.15090.03040.22313.1193-4.8216-11.0194
43.87341.0976-2.26574.4665-0.35957.23760.15890.53680.09070.1287-0.09240.6554-0.557-0.9291-0.05970.19210.04180.0430.2550.02070.21644.5312-16.5685-7.753
53.74312.1144-2.98434.3105-3.54043.51880.0194-0.04270.0743-0.1814-0.08750.03850.15410.12140.10520.1531-0.013-0.00520.1217-0.00130.140419.5836-13.9273-14.3411
67.36382.7349-3.67793.7261-1.96795.6582-0.0476-0.2188-0.05520.142-0.0675-0.2639-0.20360.35010.07580.1775-0.0231-0.01510.13670.01580.112123.3797-10.4875-7.3619
73.66984.6475-2.13455.9317-2.40493.71180.1509-0.10410.51780.3210.05840.3673-0.3715-0.1221-0.23280.24910.03430.03510.1640.01210.19312.3748-7.6353-6.4868
80.93930.4508-0.57783.4557-1.27341.76340.05430.12480.15370.09610.03090.1485-0.16370.0438-0.06740.147-0.00090.00250.16090.01920.127317.9271-12.31-17.8729
92.53173.83962.59758.07170.50148.0660.1490.08410.55330.40820.02930.103-0.88930.2082-0.07770.3322-0.02360.05140.16380.00510.223621.57571.023-20.0631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'D' and (resid 8 through 17 )
3X-RAY DIFFRACTION3chain 'D' and (resid 18 through 24 )
4X-RAY DIFFRACTION4chain 'D' and (resid 25 through 33 )
5X-RAY DIFFRACTION5chain 'D' and (resid 34 through 57 )
6X-RAY DIFFRACTION6chain 'D' and (resid 58 through 73 )
7X-RAY DIFFRACTION7chain 'D' and (resid 74 through 83 )
8X-RAY DIFFRACTION8chain 'D' and (resid 84 through 111 )
9X-RAY DIFFRACTION9chain 'D' and (resid 112 through 117 )

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