3TC8 | pdb_00003tc8

Crystal structure of a Zn-dependent exopeptidase (BDI_3547) from Parabacteroides distasonis ATCC 8503 at 1.06 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3TC8/pdb

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


• Deposited: 2011-08-08 Released: 2011-08-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 
  0.132 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.112 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Literature

Crystal structure of a Hypothetical Zn-dependent exopeptidase (BDI_3547) from Parabacteroides distasonis ATCC 8503 at 1.06 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: 68.86 kDa 
• Atom Count: 5,913 
• Modeled Residue Count: 585 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine aminopeptidase	A, B	309	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_3547
UniProt
Find proteins for A6LHT4 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LHT4  Go to UniProtKB:  A6LHT4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 1.06 Å
• R-Value Free:  0.132 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.112 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33TC8

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.662	α = 105.74
b = 51.277	β = 99.92
c = 72.985	γ = 97.46

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: 2011-08-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-27
  Changes: Data collection, Structure summary