6BA0 | pdb_00006ba0

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.218 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.200 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Pyrimidine-specific Ribonucleoside Hydrolase RihB from Gardnerella vaginalis

Renner, N., Jacques, D.A.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain E [auth A]	E [auth A], H [auth B], L [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] 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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.218 (Depositor), 0.230 (DCC)
R-Value Work: 0.186 (Depositor), 0.200 (DCC)
R-Value Observed: 0.188 (Depositor)

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Renner, N.

Jacques, D.A.

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

Revision History (Full details and data files)

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