3CMG | pdb_00003cmg

Crystal structure of putative beta-galactosidase from Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb3CMG/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-03-21 Released: 2008-04-29 
• Deposition Author(s): Ramagopal, U.A., Rutter, M., Toro, R., Hu, S., Maletic, M., Gheyi, T., 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: 1.90 Å
• R-Value Free: 
  0.186 (Depositor) 
• R-Value Work: 
  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure of putative beta-galactosidase from Bacteroides fragilis.

Ramagopal, U.A., Rutter, M., Toro, R., Hu, S., Maletic, M., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 77.17 kDa 
• Atom Count: 5,977 
• Modeled Residue Count: 661 
• Deposited Residue Count: 667 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative beta-galactosidase	A	667	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF0328 EC: 3.2.1.31
UniProt
Find proteins for Q5LIC7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LIC7  Go to UniProtKB:  Q5LIC7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth A], E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.186 (Depositor) 
• R-Value Work:  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.651	α = 90
b = 102.878	β = 90
c = 199.967	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXE	model building
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Ramagopal, U.A., Rutter, M., Toro, R., Hu, S., Maletic, M., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, 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: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references