3IMM | pdb_00003imm

Crystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IMM/pdb

• Classification: HYDROLASE
• Organism(s): Parabacteroides distasonis ATCC 8503
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-10 Released: 2009-08-18 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides distasonis ATCC 8503 at 2.00 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 Evidence: gel filtration

Biological Assembly 2  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 68.72 kDa 
• Atom Count: 5,199 
• Modeled Residue Count: 591 
• Deposited Residue Count: 603 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative secreted glycosylhydrolase	A, B, C	201	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_0489, YP_001301887.1
UniProt
Find proteins for A6L9A1 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6L9A1  Go to UniProtKB:  A6L9A1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	H [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], F [auth B], G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	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:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IMM

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.404	α = 90
b = 45.404	β = 90
c = 241.069	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary