1ATG

AZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN

• PDB DOI:  https://doi.org/10.2210/pdb1ATG/pdb

• Classification: BINDING PROTEIN
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 1997-08-14 Released: 1998-10-14 
• Deposition Author(s): Lawson, D.M., Pau, R.N., Williams, C.E.M., Mitchenall, L.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.183 
• R-Value Work: 0.164 

Literature

Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.

Lawson, D.M., Williams, C.E., Mitchenall, L.A., Pau, R.N.

(1998) Structure 6: 1529-1539

• PubMed: 9862806 
• DOI: https://doi.org/10.1016/s0969-2126(98)00151-8
• Primary Citation of Related Structures:  
  1ATG


• PubMed Abstract: 
  

  . Periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. Nevertheless, almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. The ligand is bound at the bottom of a deep cleft, which lies at the interface between these two domains. The oxyanion-binding proteins are notable in that they can discriminate between very similar ligands.

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Organizational Affiliation: 

Nitrogen Fixation Laboratory John Innes Centre Norwich NR4 7UH UK. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.92 kDa 
• Atom Count: 2,126 
• Modelled Residue Count: 231 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC MOLYBDATE-BINDING PROTEIN	A	231	Azotobacter vinelandii	Mutation(s): 0
UniProt
Find proteins for Q7SIH2 (Azotobacter vinelandii) Explore Q7SIH2  Go to UniProtKB:  Q7SIH2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WO4	B [auth A]	TUNGSTATE(VI)ION O4 W PBYZMCDFOULPGH-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.183 
• R-Value Work: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.934	α = 90
b = 88.802	β = 93.55
c = 41.746	γ = 90

Software Package:

Software Name	Purpose
VARIOUS	model building
DM	model building
O	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing
DM	phasing
OTHERS)	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Lawson, D.M., Pau, R.N., Williams, C.E.M., Mitchenall, L.A.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance