3FZX

CRYSTAL STRUCTURE OF A PUTATIVE EXPORTED PROTEIN WITH YMCC-LIKE FOLD (BF2203) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 2.22 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3FZX/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-26 Released: 2009-02-03 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.250 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Crystal structure of putative exported protein with YmcC-like fold (YP_211880.1) from Bacteroides fragilis NCTC 9343 at 2.22 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 25.28 kDa 
• Atom Count: 1,776 
• Modelled Residue Count: 212 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative exported protein	A	218	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF2257, YP_211880.1
UniProt
Find proteins for Q5LD59 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LD59  Go to UniProtKB:  Q5LD59

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 2.22 Å
• R-Value Free: 0.250 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 6₄ 2 2
• Diffraction Data: https://doi.org/10.18430/M33FZX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.74	α = 90
b = 143.74	β = 90
c = 49.46	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations