1IXH

PHOSPHATE-BINDING PROTEIN (PBP) COMPLEXED WITH PHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1IXH/pdb

• Classification: PHOSPHATE TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-08-01 Released: 1998-02-04 
• Deposition Author(s): Wang, Z., Luecke, H., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.141 
• R-Value Observed: 0.114 

Starting Model: experimental

Literature

A low energy short hydrogen bond in very high resolution structures of protein receptor--phosphate complexes.

Wang, Z., Luecke, H., Yao, N., Quiocho, F.A.

(1997) Nat Struct Biol 4: 519-522

• PubMed: 9228942 
• DOI: https://doi.org/10.1038/nsb0797-519
• Primary Citation of Related Structures:  
  1IXG, 1IXH, 1IXI


• PubMed Abstract: 
  

  A very short hydrogen bond between an Asp and a phosphate is established in two high resolution structures (0.98 and 1.05 A). A mutant complex that changes the Asp to an Asn, which forms a normal hydrogen bond, has a similar free energy of binding to the wild type complex, suggesting that the contribution of the short hydrogen bond is not extraordinarily strong.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.55 kDa 
• Atom Count: 2,453 
• Modelled Residue Count: 321 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHATE-BINDING PROTEIN	A	321	Escherichia coli	Mutation(s): 0  Gene Names: PHO-S
UniProt
Find proteins for P0AG82 (Escherichia coli (strain K12)) Explore P0AG82  Go to UniProtKB:  P0AG82

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.141 
• R-Value Observed: 0.114 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.506	α = 90
b = 63.379	β = 90
c = 122.373	γ = 90

Software Package:

Software Name	Purpose
SHELXL-96	model building
SHELXL-96	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXL-96	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-04 
Deposition Author(s): Wang, Z., Luecke, H., Quiocho, F.A.

Revision History  

• Version 1.0: 1998-02-04
  Type: Initial release
  
• Version 1.1: 2008-03-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection