1IXI

PHOSPHATE-BINDING PROTEIN MUTANT WITH ASP 56 REPLACED BY ASN COMPLEX WITH MONOBASIC PHOSPHATE ION

• PDB DOI:  https://doi.org/10.2210/pdb1IXI/pdb

• Classification: PHOSPHATE TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-10-17 Released: 1997-10-22 
• Deposition Author(s): Wang, Z., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.294 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

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.

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Related Citations: 

• Negative Electrostatic Surface Potential of Protein Sites Specific for Anionic Ligands
  Ledvina, P.S., Yao, N., Choudhary, A., Quiocho, F.A.
  (1996) Proc Natl Acad Sci U S A 93: 6786

• Modulation of a Salt Link Does not Affect Binding of Phosphate to its Specific Active Transport Receptor
  Yao, N., Ledvina, P.S., Choudhary, A., Quiocho, F.A.
  (1996) Biochemistry 35: 2079

• Fine Tuning the Specificity of the Periplasmic Phosphate Transport Receptor. Site-Directed Mutagenesis, Ligand Binding, and Crystallographic Studies
  Wang, Z., Choudhary, A., Ledvina, P.S., Quiocho, F.A.
  (1994) J Biol Chem 269: 25091

• The Immunodominant 38-kDa Lipoprotein Antigen of Mycobacterium Tuberculosis is a Phosphate-Binding Protein
  Chang, Z., Choudhary, A., Lathigra, R., Quiocho, F.A.
  (1994) J Biol Chem 269: 1956

• High Specificity of a Phosphate Transport Protein Determined by Hydrogen Bonds
  Luecke, H., Quiocho, F.A.
  (1990) Nature 347: 402

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Organizational Affiliation: 

RIKEN Yokoyama Laboratory, Yokohama, 230-0045, Japan.

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: 2,654 
• 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): 1  Gene Names: POTENTIAL
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
2HP	B [auth A]	DIHYDROGENPHOSPHATE ION H2 O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
2HP	Binding MOAD:  1IXI	Kd: 360 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.294 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.97	α = 90
b = 63.98	β = 90
c = 123.97	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
UCSD	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-10-22 
Deposition Author(s): Wang, Z., Quiocho, F.A.

Revision History  

• Version 1.0: 1997-10-22
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other