4GL3 | pdb_00004gl3

Crystal structure of a putative glucoamylase (BACUNI_03963) from Bacteroides uniformis ATCC 8492 at 2.01 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4GL3/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides uniformis ATCC 8492
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-13 Released: 2012-08-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Literature

Crystal structure of a putative glucoamylase (BACUNI_03963) from Bacteroides uniformis ATCC 8492 at 2.01 A resolution

Joint Center for Structural Genomics (JCSG)

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: 49.41 kDa 
• Atom Count: 3,811 
• Modeled Residue Count: 412 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative glucoamylase	A	424	Bacteroides uniformis ATCC 8492	Mutation(s): 0  Gene Names: BACUNI_03963

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.01 Å
• R-Value Free:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34GL3

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.568	α = 90
b = 121.568	β = 90
c = 267.888	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary