3DV6

Crystal structure of SAG506-01, tetragonal, crystal 2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 

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This is version 1.2 of the entry. See complete history. 


Literature

Pseudo-symmetry and twinning in crystals of homologous antibody Fv fragments.

Brooks, C.L., Blackler, R.J., Gerstenbruch, S., Kosma, P., Muller-Loennies, S., Brade, H., Evans, S.V.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1250-1258

  • DOI: 10.1107/S0907444908033453
  • Primary Citation of Related Structures:  
    3DUU, 3DV6, 3DUR, 3DUS, 3DV4

  • PubMed Abstract: 

    • A difference of seven conservative amino-acid substitutions between two single-chain antibodies (scFvs) specific for chlamydial lipopolysaccharide does not significantly affect their molecular structures or packing contacts, but dramatically affects ...

    A difference of seven conservative amino-acid substitutions between two single-chain antibodies (scFvs) specific for chlamydial lipopolysaccharide does not significantly affect their molecular structures or packing contacts, but dramatically affects their crystallization. The structure of the variable domain (Fv) of SAG173-04 was solved to 1.86 A resolution and an R(cryst) of 18.9% in space group P2(1)2(1)2(1). Crystals of the homologous SAG506-01 diffracted to 1.95 A resolution and appeared at first to have Patterson symmetry I4/m or P4/mmm; however, no solution could be found in space groups belonging to the former and refinement in the only solution corresponding to the latter (in space group P4(3)2(1)2) stalled at R(free) = 30.0%. Detailed examination of the diffraction data revealed that the crystal was likely to be twinned and that the correct space group was P2(1)2(1)2(1). Both translational pseudo-symmetry and pseudo-merohedral twinning were observed in one crystal of SAG506-01 and pseudo-merohedral twinning was observed for a second crystal. The final R factor for SAG506-01 after refinement in P2(1)2(1)2(1) was 20.5%.

    Organizational Affiliation: 

    University of Victoria, Department of Biochemistry and Microbiology, Victoria BC V8P 3P6, Canada.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
antibody Fv fragment SAG506-01A112Mus musculusMutation(s): 0 
Gene Names: Vk
Find proteins for A0N262 (Mus musculus)
Explore A0N262 
Go to UniProtKB:  A0N262
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ig-like proteinB121Mus musculusMutation(s): 0 
Find proteins for A2NU21 (Mus musculus)
Explore A2NU21 
Go to UniProtKB:  A2NU21
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KDO
Query on KDO
Download Ideal Coordinates CCD File 
B
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.42α = 90
b = 71.42β = 90
c = 85.08γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary