2C0Z | pdb_00002c0z

The 1.6 A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides

• PDB DOI: https://doi.org/10.2210/pdb2C0Z/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces niveus NCIMB 11891
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-09 Released: 2006-01-25 
• Deposition Author(s): Jakimowicz, P., Tello, M., Freel-Meyers, C.L., Walsh, C.T., Buttner, M.J., Field, R.A., Lawson, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.195 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.150 (Depositor) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

The 1.6 A Resolution Crystal Structure of Novw: A 4-Keto-6-Deoxy Sugar Epimerase from the Novobiocin Biosynthetic Gene Cluster of Streptomyces Spheroides

Jakimowicz, P., Tello, M., Freel-Meyers, C.L., Walsh, C.T., Buttner, M.J., Field, R.A., Lawson, D.M.

(2006) Proteins 63: 261

• PubMed: 16411240 
• DOI: https://doi.org/10.1002/prot.20818
• Primary Citation Related Structures: 
  2C0Z

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Organizational Affiliation: 
• Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 23.49 kDa 
• Atom Count: 1,738 
• Modeled Residue Count: 199 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NOVW	A	216	Streptomyces niveus NCIMB 11891	Mutation(s): 0  EC: 5.1.3
UniProt
Find proteins for Q9L9E5 (Streptomyces niveus) Explore Q9L9E5  Go to UniProtKB:  Q9L9E5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.195 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.150 (Depositor) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.354	α = 90
b = 59.354	β = 90
c = 109.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-25 
Deposition Author(s): Jakimowicz, P., Tello, M., Freel-Meyers, C.L., Walsh, C.T., Buttner, M.J., Field, R.A., Lawson, D.M.

Revision History  

• Version 1.0: 2006-01-25
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
• Version 1.2: 2014-03-12
  Changes: Source and taxonomy
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description