5XJW | pdb_00005xjw

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 (Depositor), 0.249 (DCC)
R-Value Work:
0.225 (Depositor), 0.228 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

Macromolecule Content

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

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(TPTPCPGPCPCPGPCPCPGPAPA)-3')	A, B	13	synthetic construct
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G79611HT GlyCosmos: G79611HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G63753LU GlyCosmos: G63753LU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPH Query on CPH Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	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		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], K [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B]

Biologically Interesting Molecules (External Reference)

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001136 Query on PRD_001136	C, F	Chromomycin A3, Monomer	Oligosaccharide / Antibiotic		Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001136 Query on PRD_001136	D, E	Chromomycin A3, Monomer	Oligosaccharide / Antibiotic		Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.246 (Depositor), 0.249 (DCC)
R-Value Work: 0.225 (Depositor), 0.228 (DCC)
R-Value Observed: 0.228 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

This entry supersedes: 5ES0

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