7LTB

Crystal Structure of Keratinicyclin B

• PDB DOI: https://doi.org/10.2210/pdb7LTB/pdb

• Classification: ANTIBIOTIC
• Organism(s): Amycolatopsis keratiniphila
• Mutation(s): No 


• Deposited: 2021-02-19 Released: 2022-12-07 
• Deposition Author(s): Davis, K.M., Jeffrey, P.D., Seyedsayamdost, M.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.151 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 

Literature

Structural and Functional Analysis of Keratinicyclin Reveals Synergistic Antibiosis with Vancomycin against Clostridium difficile

McWhorter, K.L., Chioti, V.T., Xu, F., Jeffrey, P.D., Davis, K.M., Seyedsayamdost, M.R.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.44 kDa 
• Atom Count: 277 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Keratinicyclin B peptide moiety	A, B	6	Amycolatopsis keratiniphila	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
3-ammonio-2,3,6-trideoxy-alpha-L-arabino-hexopyranose-(1-2)-beta-D-glucopyranose	C [auth F], D [auth J]	2		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN (Subject of Investigation/LOI)	E [auth A], G [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
YBJ (Subject of Investigation/LOI)	F [auth A], H [auth B]	(2~{S},4~{S},5~{R},6~{S})-4-azanyl-5-methoxy-6-methyl-oxan-2-ol C7 H15 N O3 ZECQVPSAXSIXIC-KQXJUZEQSA-N
FMT (Subject of Investigation/LOI)	I [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMY	A, B	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 0.151 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.316	α = 90
b = 29.667	β = 90
c = 32.209	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Davis, K.M., Jeffrey, P.D., Seyedsayamdost, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM129496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	4R00GM129460

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations