6BA0

Pyrimidine-specific Ribonucleoside Hydrolase from Gardnerella vaginalis

• PDB DOI: https://doi.org/10.2210/pdb6BA0/pdb

• Classification: HYDROLASE
• Organism(s): Gardnerella vaginalis 315-A
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-10-11 Released: 2018-10-17 
• Deposition Author(s): Renner, N., Jacques, D.A.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Pyrimidine-specific Ribonucleoside Hydrolase RihB from Gardnerella vaginalis

Renner, N., Jacques, D.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 137.18 kDa 
• Atom Count: 10,271 
• Modelled Residue Count: 1,232 
• Deposited Residue Count: 1,260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidine/uridine-specific hydrolase	A, B, C, D	315	Gardnerella vaginalis 315-A	Mutation(s): 0  Gene Names: rihA, HMPREF9435_0920 EC: 3.2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], H [auth B], L [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.07	α = 90
b = 79.36	β = 99.62
c = 115.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Renner, N., Jacques, D.A.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1036521

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description