4QYM

The crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with methionine

• PDB DOI: https://doi.org/10.2210/pdb4QYM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Trichormus variabilis ATCC 29413
• Mutation(s): Yes 


• Deposited: 2014-07-24 Released: 2014-08-13 
• Deposition Author(s): Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.212 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

The crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with methionine

Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.31 kDa 
• Atom Count: 6,128 
• Modelled Residue Count: 728 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid/amide ABC transporter substrate-binding protein, HAAT family	A, B	395	Trichormus variabilis ATCC 29413	Mutation(s): 1  Gene Names: Ava_0465
UniProt
Find proteins for Q3MFZ5 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3MFZ5  Go to UniProtKB:  Q3MFZ5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MET	C [auth A], F [auth B]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
VAL	D [auth A], G [auth B]	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.212 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.964	α = 90
b = 97.555	β = 90
c = 150.151	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection