5FCC | pdb_00005fcc

Structure of HutD from Pseudomonas fluorescens SBW25 (NaCl condition)

• PDB DOI: https://doi.org/10.2210/pdb5FCC/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pseudomonas [fluorescens] SBW25
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-15 Released: 2017-01-25 
• Deposition Author(s): Johnston, J.M., Gerth, M.L., Baker, E.N., Lott, J.S., Rainey, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structure of HutD from Pseudomonas fluorescens

Gerth, M.L., Liu, Y.H., Zhang, X.-X., Baker, E.N., Lott, J.S., Rainey, P.B., Johnston, J.M.

To be published.

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: 42.85 kDa 
• Atom Count: 3,134 
• Modeled Residue Count: 370 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HutD	A, B	193	Pseudomonas [fluorescens] SBW25	Mutation(s): 0  Gene Names: PFLU_0360
UniProt
Find proteins for C3K802 (Pseudomonas fluorescens (strain SBW25)) Explore C3K802  Go to UniProtKB:  C3K802

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A], F [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.998	α = 90
b = 81.998	β = 90
c = 169.901	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Johnston, J.M., Gerth, M.L., Baker, E.N., Lott, J.S., Rainey, P.B.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Data collection, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description