6ZJG | pdb_00006zjg

Crystal structure of ACPA E4 in complex with CII-C-48-CIT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.230 (DCC) 

Starting Model: experimental
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This is version 3.2 of the entry. See complete history. 


Literature

Crystal structure of ACPA E4 in complex with CII-C-48-CIT

Ge, C., Rikard, H.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CII-C-48-CITA [auth B]18Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACPA E4 Fab fragment - heavy chainB [auth HHH]221Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACPA E4 Fab fragment - light chainC [auth LLL]216Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CIR
Query on CIR		A [auth B]L-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.183α = 90
b = 151.774β = 90
c = 97.066γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 2.0: 2022-12-07
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description
  • Version 3.1: 2024-01-31
    Changes: Refinement description
  • Version 3.2: 2024-10-16
    Changes: Structure summary