4QT9 | pdb_00004qt9

Crystal structure of a putative glucoamylase (BACCAC_03554) from Bacteroides caccae ATCC 43185 at 2.05 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4QT9/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides caccae ATCC 43185
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-07 Released: 2014-08-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.220 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of a putative glucoamylase (BACCAC_03554) from Bacteroides caccae ATCC 43185 at 2.05 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 100.82 kDa 
• Atom Count: 7,283 
• Modeled Residue Count: 827 
• Deposited Residue Count: 878 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative glucoamylase	A, B	439	Bacteroides caccae ATCC 43185	Mutation(s): 0  Gene Names: BACCAC_03554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	G [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ACT	C [auth A], D [auth A], E [auth B], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.220 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34QT9

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.925	α = 90
b = 80.728	β = 90
c = 90.752	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2017-11-22
  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: 2024-10-16
  Changes: Data collection, Structure summary