3NYI | pdb_00003nyi

The crystal structure of a fat acid (stearic acid)-binding protein from Eubacterium ventriosum ATCC 27560.

• PDB DOI: https://doi.org/10.2210/pdb3NYI/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Eubacterium ventriosum ATCC 27560
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-15 Released: 2010-09-22 
• Deposition Author(s): Zhang, R., Tan, K., Li, H., Keigher, L., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.220 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

The crystal structure of a fat acid (stearic acid)-binding protein from Eubacterium ventriosum ATCC 27560.

Zhang, R., Tan, K., Li, H., Keigher, L., Babnigg, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.71 kDa 
• Atom Count: 4,990 
• Modeled Residue Count: 588 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fat acid-binding protein	A, B	296	Eubacterium ventriosum ATCC 27560	Mutation(s): 0  Gene Names: EUBVEN_01190
UniProt
Find proteins for A5Z657 (Eubacterium ventriosum ATCC 27560) Explore A5Z657  Go to UniProtKB:  A5Z657

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STE	C [auth A], D [auth B]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-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: 1.90 Å
• R-Value Free:  0.220 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.725	α = 90
b = 110.221	β = 108.62
c = 57.127	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Zhang, R., Tan, K., Li, H., Keigher, L., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-21
  Changes: Structure summary
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary