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- PDB-5e7b: Structure of a nanobody (vHH) from camel against phage Tuc2009 RB... -

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Basic information

Entry
Database: PDB / ID: 5e7b
TitleStructure of a nanobody (vHH) from camel against phage Tuc2009 RBP (BppL, ORF53)
Componentsnanobody nano-L06
KeywordsIMMUNE SYSTEM / bacteriophages / Lactococcus lactis / receptor binding protein / single-chain nanobody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsLegrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. ...Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C.
CitationJournal: Mbio / Year: 2016
Title: The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules.
Authors: Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Structure summary
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3May 4, 2016Group: Database references
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nanobody nano-L06


Theoretical massNumber of molelcules
Total (without water)14,1641
Polymers14,1641
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.080, 52.080, 162.690
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
11A-314-

HOH

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Components

#1: Antibody nanobody nano-L06


Mass: 14164.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: obtained upon immunization / Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN6 / Production host: Escherichia coli BL21 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: mixing 100-300 nl of 12 mg.mL-1 protein (Na2HPO4, 10 mM; KH2PO4, 1.8 mM, pH7.4; NaCl, 137 mM; KCl, 2.7mM) with 100 nl precipitant solution in 25-30 % PEG4000, 0.2 M Imidazole (pH 6.0).
PH range: 7.2 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.86 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 1.1→45.1 Å / Num. all: 51977 / Num. obs: 52014 / % possible obs: 96.6 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.4
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 19.2 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 1.5 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
SHELXphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.1→14.97 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1892 4719 4.87 %
Rwork0.158 --
obs0.1595 96986 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 0 185 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011094
X-RAY DIFFRACTIONf_angle_d1.3671504
X-RAY DIFFRACTIONf_dihedral_angle_d13.131395
X-RAY DIFFRACTIONf_chiral_restr0.08165
X-RAY DIFFRACTIONf_plane_restr0.006201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11250.30591520.3162905X-RAY DIFFRACTION91
1.1125-1.12560.30751520.27022939X-RAY DIFFRACTION93
1.1256-1.13930.25611590.25362999X-RAY DIFFRACTION95
1.1393-1.15370.27011560.23463021X-RAY DIFFRACTION95
1.1537-1.16890.25361570.23752999X-RAY DIFFRACTION95
1.1689-1.18490.27161630.23343067X-RAY DIFFRACTION95
1.1849-1.20180.27251560.2282958X-RAY DIFFRACTION95
1.2018-1.21980.25861630.22273060X-RAY DIFFRACTION96
1.2198-1.23880.25891650.2243039X-RAY DIFFRACTION96
1.2388-1.25910.25031600.21152999X-RAY DIFFRACTION96
1.2591-1.28080.28591620.19883052X-RAY DIFFRACTION96
1.2808-1.30410.19311580.19913104X-RAY DIFFRACTION96
1.3041-1.32910.22761580.19143043X-RAY DIFFRACTION96
1.3291-1.35630.2221570.19293039X-RAY DIFFRACTION96
1.3563-1.38570.21541660.18793076X-RAY DIFFRACTION97
1.3857-1.41790.2081610.17593066X-RAY DIFFRACTION97
1.4179-1.45340.17731660.16093114X-RAY DIFFRACTION97
1.4534-1.49260.19551640.16893069X-RAY DIFFRACTION97
1.4926-1.53650.19221630.16333109X-RAY DIFFRACTION97
1.5365-1.58610.15351630.15433083X-RAY DIFFRACTION98
1.5861-1.64270.18111670.14913120X-RAY DIFFRACTION98
1.6427-1.70840.18181590.15123102X-RAY DIFFRACTION98
1.7084-1.7860.17411630.14713117X-RAY DIFFRACTION98
1.786-1.880.15411640.14573150X-RAY DIFFRACTION99
1.88-1.99750.1647930.13713205X-RAY DIFFRACTION99
1.9975-2.15130.12641200.13833190X-RAY DIFFRACTION99
2.1513-2.36710.16681570.14033159X-RAY DIFFRACTION99
2.3671-2.70780.16641620.15433142X-RAY DIFFRACTION99
2.7078-3.40490.18051600.15163172X-RAY DIFFRACTION100
3.4049-14.97180.20761730.14483169X-RAY DIFFRACTION100

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