3H75 | pdb_00003h75

Crystal Structure of a Periplasmic Sugar-binding protein from the Pseudomonas fluorescens

• PDB DOI: https://doi.org/10.2210/pdb3H75/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas protegens Pf-5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-24 Released: 2009-05-12 
• Deposition Author(s): Kumaran, D., Mahmood, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal Structure of a Periplasmic Sugar-binding protein from the Pseudomonas fluorescens

Kumaran, D., Mahmood, A., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.92 kDa 
• Atom Count: 2,885 
• Modeled Residue Count: 328 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic sugar-binding domain protein	A	350	Pseudomonas protegens Pf-5	Mutation(s): 0  Gene Names: PFL_3664
UniProt
Find proteins for Q4KAG7 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KAG7  Go to UniProtKB:  Q4KAG7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.526	α = 90
b = 81.275	β = 90
c = 63.082	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Kumaran, D., Mahmood, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary