5XJW

Crystal Structure of the [Co2+-(Chromomycin A3)2]-CCG repeats Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.246 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPHClick on this verticalbar to view details

This is version 3.1 of the entry. See complete history


Literature

Crystal Structure of the [Co2+-(Chromomycin A3)2]-CCG repeats Complex

Tseng, W.H.Wu, P.C.Satange, R.B.Hou, M.H.

To be published.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')
A, B
13synthetic construct
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose
C, F
3N/A
Glycosylation Resources
GlyTouCan:  G79611HT
GlyCosmos:  G79611HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose
D, E
2N/A
Glycosylation Resources
GlyTouCan:  G63753LU
GlyCosmos:  G63753LU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.309α = 90
b = 48.309β = 90
c = 83.636γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data processing
SCALEPACKdata scaling
PHENIXmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 2.0: 2018-06-06
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2018-09-12
    Changes: Data collection, Structure summary
  • Version 2.2: 2018-10-03
    Changes: Data collection, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary