4MO9 | pdb_00004mo9

Crystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula

• PDB DOI: https://doi.org/10.2210/pdb4MO9/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Veillonella parvula DSM 2008
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-11 Released: 2013-09-25 
• Deposition Author(s): Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula

Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 41.84 kDa 
• Atom Count: 2,964 
• Modeled Residue Count: 349 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A	369	Veillonella parvula DSM 2008	Mutation(s): 0  Gene Names: Vpar_0195
UniProt
Find proteins for A0ABF7PFP3 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / CCUG 5123 / JCM 12972 / NCTC 11810 / Te3)) Explore A0ABF7PFP3  Go to UniProtKB:  A0ABF7PFP3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
TMO	B [auth A]	trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.402	α = 90
b = 75.999	β = 90
c = 125.187	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary