3N6Z | pdb_00003n6z

Crystal structure of a putative immunoglobulin A1 protease (BACOVA_03286) from Bacteroides ovatus at 1.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3N6Z/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides ovatus ATCC 8483
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-26 Released: 2010-07-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.157 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

Crystal structure of a putative immunoglobulin A1 protease (BACOVA_03286) from Bacteroides ovatus at 1.30 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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.43 kDa 
• Atom Count: 3,166 
• Modeled Residue Count: 339 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative immunoglobulin A1 protease	A	363	Bacteroides ovatus ATCC 8483	Mutation(s): 0  Gene Names: BACOVA_03286

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [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: 1.30 Å
• R-Value Free:  0.157 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33N6Z

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.679	α = 90
b = 75.679	β = 90
c = 132.101	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Structure summary