3FFY | pdb_00003ffy

Putative tetrapyrrole (corrin/porphyrin) methyltransferase from Bacteroides fragilis.

• PDB DOI: https://doi.org/10.2210/pdb3FFY/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-04 Released: 2008-12-16 
• Deposition Author(s): Osipiuk, J., Volkart, L., Cobb, G., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

X-ray crystal structure of putative tetrapyrrole (corrin/porphyrin) methyltransferase from Bacteroides fragilis.

Osipiuk, J., Volkart, L., Cobb, G., Kim, Y., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.25 kDa 
• Atom Count: 977 
• Modeled Residue Count: 112 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tetrapyrrole (Corrin/porphyrin) methylase	A	115	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF0585 EC: 2.1.1.198
UniProt
Find proteins for Q5LHP3 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LHP3  Go to UniProtKB:  Q5LHP3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.536	α = 90
b = 60.536	β = 90
c = 96.065	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-16 
Deposition Author(s): Osipiuk, J., Volkart, L., Cobb, G., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-12-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary