2PYX

Crystal structure of tryptophan halogenase (YP_750003.1) from Shewanella frigidimarina NCIMB 400 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PYX/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Shewanella frigidimarina NCIMB 400
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-16 Released: 2007-05-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Literature

Crystal structure of tryptophan halogenase (YP_750003.1) from Shewanella frigidimarina NCIMB 400 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 119.85 kDa 
• Atom Count: 10,168 
• Modelled Residue Count: 1,052 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan halogenase	A, B	526	Shewanella frigidimarina NCIMB 400	Mutation(s): 9  Gene Names: YP_750003.1, Sfri_1312
UniProt
Find proteins for Q085A0 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q085A0  Go to UniProtKB:  Q085A0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth A], I [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
TLA	D [auth A], E [auth A], G [auth B], H [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.181 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M32PYX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.545	α = 90
b = 109.613	β = 90
c = 120.036	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2023-01-25
  Changes: Database references, Derived calculations