4RV5 | pdb_00004rv5

The crystal structure of a solute-binding protein from Anabaena variabilis ATCC 29413 in complex with pyruvic acid

• PDB DOI: https://doi.org/10.2210/pdb4RV5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Trichormus variabilis ATCC 29413
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-24 Released: 2014-12-10 
• 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: 1.04 Å
• R-Value Free: 
  0.131 (Depositor), 0.133 (DCC) 
• R-Value Work: 
  0.112 (Depositor), 0.114 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Literature

The crystal structure of a solute-binding protein from Anabaena variabilis ATCC 29413 in complex with pyruvic acid

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 kDa 
• Atom Count: 6,675 
• Modeled 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): 0  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
PYR	C [auth A], F [auth B]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
FMT	E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	D [auth A], G [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: 1.04 Å
• R-Value Free:  0.131 (Depositor), 0.133 (DCC) 
• R-Value Work:  0.112 (Depositor), 0.114 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.525	α = 90
b = 100.588	β = 90
c = 150.602	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-11-27
  Changes: Structure summary