3VXD | pdb_00003vxd

Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus agalactiae

• PDB DOI: https://doi.org/10.2210/pdb3VXD/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus agalactiae NEM316
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-11 Released: 2012-10-03 
• Deposition Author(s): Nakamichi, Y., Maruyama, Y., Mikami, B., Hashimoto, W., Murata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus agalactiae

Nakamichi, Y., Maruyama, Y., Mikami, B., Hashimoto, W., Murata, K.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 187.14 kDa 
• Atom Count: 12,955 
• Modeled Residue Count: 1,424 
• Deposited Residue Count: 1,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein gbs1889	A, B, C, D	398	Streptococcus agalactiae NEM316	Mutation(s): 1  Gene Names: gbs1889 EC: 3.2.1 (PDB Primary Data), 3.2.1.180 (UniProt)
UniProt
Find proteins for Q8E372 (Streptococcus agalactiae serotype III (strain NEM316)) Explore Q8E372  Go to UniProtKB:  Q8E372

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C], H [auth C], I [auth D], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.074	α = 90
b = 95.914	β = 104.06
c = 110.886	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Nakamichi, Y., Maruyama, Y., Mikami, B., Hashimoto, W., Murata, K.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description