5XJW

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

• PDB DOI: https://doi.org/10.2210/pdb5XJW/pdb
• Entry: 5XJW supersedes: 5ES0
• NAKB: 5XJW

• Classification: DNA/ANTIBIOTIC
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-05-04 Released: 2018-05-16 
• Deposition Author(s): Tseng, W.H., Wu, P.C., Satange, R.B., Hou, M.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 

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.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.44 kDa 
• Atom Count: 699 
• Modelled Residue Count: 24 
• Deposited Residue Count: 26 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')	A, B	13	synthetic construct

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose	C, F	3		N/A
Glycosylation Resources
GlyTouCan:  G79611HT GlyCosmos:  G79611HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose	D, E	2		N/A
Glycosylation Resources
GlyTouCan:  G63753LU GlyCosmos:  G63753LU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPH	G [auth A], J [auth B]	(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose C21 H24 O9 AOCJXLJIUYHXRS-PKRZCTMMSA-N
CO	H [auth A], I [auth A], K [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001136	C, F	Chromomycin A3, Monomer	Oligosaccharide / Antibiotic

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001136	D, E	Chromomycin A3, Monomer	Oligosaccharide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.225 
• R-Value Observed: 0.228 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.309	α = 90
b = 48.309	β = 90
c = 83.636	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data processing
SCALEPACK	data scaling
PHENIX	model building
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Tseng, W.H., Wu, P.C., Satange, R.B., Hou, M.H.
• This entry supersedes: 5ES0

Revision History  

• 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