3E8V | pdb_00003e8v

Crystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb3E8V/pdb

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


• Deposited: 2008-08-20 Released: 2008-09-02 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.243 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis

Bonanno, J.B., Rutter, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.92 kDa 
• Atom Count: 606 
• Modeled Residue Count: 82 
• Deposited Residue Count: 82 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible transglutaminase-family protein	A	82	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF1045
UniProt
Find proteins for Q5LGG0 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LGG0  Go to UniProtKB:  Q5LGG0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNL	B [auth A]	Unknown ligand

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.243 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.006	α = 90
b = 82.006	β = 90
c = 32.367	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Hu, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references