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- PDB-1sjv: Three-Dimensional Structure of a Llama VHH Domain Swapping -

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Basic information

Entry
Database: PDB / ID: 1sjv
TitleThree-Dimensional Structure of a Llama VHH Domain Swapping
Componentsr9
KeywordsANTIBIOTIC / Camelids antibody / domain swapping / heavy chain antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSpinelli, S. / Desmyter, A. / Frenken, L. / Verrips, T. / Cambillau, C.
CitationJournal: Febs Lett. / Year: 2004
Title: Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure.
Authors: Spinelli, S. / Desmyter, A. / Frenken, L. / Verrips, T. / Tegoni, M. / Cambillau, C.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: r9


Theoretical massNumber of molelcules
Total (without water)12,6401
Polymers12,6401
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: r9

A: r9


Theoretical massNumber of molelcules
Total (without water)25,2802
Polymers25,2802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_554-x+1/4,z+3/4,y-3/41
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area12130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.3, 124.3, 124.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-138-

HOH

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Components

#1: Antibody r9


Mass: 12640.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: llama VHH single domain antibody / Source: (gene. exp.) Lama glama (llama) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): VWK18 / References: GenBank: 4165546
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.59 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 26-28% PEG 600, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.067 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.067 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 12491 / % possible obs: 98.6 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094
Reflection shellResolution: 1.94→2.01 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 974 -random
Rwork0.206 ---
all0.207 11053 --
obs0.206 11053 98.34 %-
Refinement stepCycle: LAST / Resolution: 1.94→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 0 59 855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.7

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