5V00

Structure of HutD from Pseudomonas fluorescens SBW25 (Formate condition)

• PDB DOI: https://doi.org/10.2210/pdb5V00/pdb
• Entry: 5V00 supersedes: 3ESG

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


• Deposited: 2017-02-27 Released: 2017-03-15 
• Deposition Author(s): Liu, Y., Johnston, J.M., Gerth, M.L., Baker, E.N., Lott, J.S., Rainey, P.B.
• Funding Organization(s): Foundation for Research Science and Technology, Health Research Council (HRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

Crystal structure of a bicupin protein HutD involved in histidine utilization in Pseudomonas.

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

(2017) Proteins 85: 1580-1588

• PubMed: 28383128 
• DOI: https://doi.org/10.1002/prot.25303
• Primary Citation of Related Structures:  
  5V00


• PubMed Abstract: 
  

  Cupins form one of the most functionally diverse superfamilies of proteins, with members performing a wide range of catalytic, non-catalytic, and regulatory functions. HutD is a predicted bicupin protein that is involved in histidine utilization (Hut) in Pseudomonas species. Previous genetic analyses have suggested that it limits the upper level of Hut pathway expression, but its mechanism of action is unknown. Here, we have determined the structure of PfluHutD at 1.74 Å resolution in several crystallization conditions, and identified N-formyl-l-glutamate (FG, a Hut pathway intermediate) as a potential ligand in vivo. Proteins 2017; 85:1580-1588. © 2017 Wiley Periodicals, Inc.

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Organizational Affiliation: 

New Zealand Institute for Advanced Study, Massey University Albany, Auckland, New Zealand.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.14 kDa 
• Atom Count: 3,339 
• Modelled Residue Count: 369 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.196 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.863	α = 90
b = 82.863	β = 90
c = 174.419	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-15 
Deposition Author(s): Liu, Y., Johnston, J.M., Gerth, M.L., Baker, E.N., Lott, J.S., Rainey, P.B.
• This entry supersedes: 3ESG

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Funding Organization	Location	Grant Number
Foundation for Research Science and Technology	New Zealand	--
Health Research Council (HRC)	New Zealand	--

Revision History  

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-04-19
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Database references
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description