2JKC | pdb_00002jkc

Crystal Structure of E346D of Tryptophan 7-Halogenase (PrnA)

• PDB DOI: https://doi.org/10.2210/pdb2JKC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas fluorescens
• Expression System: Pseudomonas fluorescens
• Mutation(s): Yes 


• Deposited: 2008-08-26 Released: 2008-09-02 
• Deposition Author(s): Zhu, X., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

New insights into the mechanism of enzymatic chlorination of tryptophan.

Flecks, S., Patallo, E.P., Zhu, X., Ernyei, A.J., Seifert, G., Schneider, A., Dong, C., Naismith, J.H., van Pee, K.H.

(2008) Angew Chem Int Ed Engl 47: 9533-9536

• PubMed: 18979475 
• DOI: https://doi.org/10.1002/anie.200802466
• Primary Citation Related Structures: 
  2JKC

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Organizational Affiliation: 
• Biochemie, TU Dresden, 01062 Dresden, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.19 kDa 
• Atom Count: 4,645 
• Modeled Residue Count: 516 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent tryptophan halogenase PrnA	A	538	Pseudomonas fluorescens	Mutation(s): 1  Gene Names: prnA EC: 1.14.19.9
UniProt
Find proteins for P95480 (Pseudomonas fluorescens) Explore P95480  Go to UniProtKB:  P95480

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TRP	B [auth A]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.36	α = 90
b = 68.36	β = 90
c = 276.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Zhu, X., Naismith, J.H.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-08-29
  Changes: Database references
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2018-10-03
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.5: 2020-03-04
  Changes: Derived calculations, Other
• Version 1.6: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description