6VWR | pdb_00006vwr

X-ray structure of clavaminate synthase with vanadyl, succinate, and deoxyguanidinoproclavaminic acid

• PDB DOI: https://doi.org/10.2210/pdb6VWR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces antibioticus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-02-20 Released: 2021-02-24 
• Deposition Author(s): Boal, A.K., Vavra, J.
• 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: 1.50 Å
• R-Value Free: 
  0.196 (Depositor) 
• R-Value Work: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of clavaminate synthase with vanadyl, succinate, and deoxyguanidinoproclavaminic acid

Vavra, J., Dunham, N.P., Krebs, C., Boal, A.K., Bollinger, J.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.78 kDa 
• Atom Count: 2,964 
• Modeled Residue Count: 323 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clavaminate synthase 3	A	346	Streptomyces antibioticus	Mutation(s): 0  Gene Names: cas3 EC: 1.14.11.21
UniProt
Find proteins for I0CBY7 (Streptomyces antibioticus) Explore I0CBY7  Go to UniProtKB:  I0CBY7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCX	C [auth A]	DEOXYGUANIDINOPROCLAVAMINIC ACID C9 H16 N4 O3 UYADDEKIZFRINK-LURJTMIESA-N
SIN	B [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
VVO	D [auth A]	oxovanadium(2+) O V MHHDXUNFNAZUGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.196 (Depositor) 
• R-Value Work:  0.175 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.288	α = 90
b = 79.288	β = 90
c = 105.573	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Currently 6VWR does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Boal, A.K., Vavra, J.

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

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Author supporting evidence, Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Refinement description