6BA1 | pdb_00006ba1

Purine-Preferring Ribonucleoside Hydrolase from Gardnerella vaginalis

PDB DOI: https://doi.org/10.2210/pdb6BA1/pdb

Classification: HYDROLASE
Organism(s): Gardnerella vaginalis 315-A
Expression System: Escherichia coli BL21(DE3)
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: 2.90 Å
R-Value Free:
0.282 (Depositor), 0.277 (DCC)
R-Value Work:
0.279 (Depositor), 0.276 (DCC)
R-Value Observed:
0.279 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Inosine-Uridine Preferring Ribonucleoside Hydrolase from Gardnerella vaginalis

Renner, N., Jacques, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 620.58 kDa
Atom Count: 42,469
Modeled Residue Count: 5,688
Deposited Residue Count: 5,778
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-uridine preferring nucleoside hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	321	Gardnerella vaginalis 315-A	Mutation(s): 0 Gene Names: HMPREF9435_1145 EC: 3.2.2.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain BA [auth J] SDF format, chain CA [auth K] SDF format, chain DA [auth L] SDF format, chain EA [auth M] SDF format, chain FA [auth N] SDF format, chain GA [auth O] SDF format, chain HA [auth P] SDF format, chain IA [auth Q] SDF format, chain JA [auth R] SDF format, chain S [auth A] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain V [auth D] SDF format, chain W [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth H] MOL2 format, chain AA [auth I] MOL2 format, chain BA [auth J] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain FA [auth N] MOL2 format, chain GA [auth O] MOL2 format, chain HA [auth P] MOL2 format, chain IA [auth Q] MOL2 format, chain JA [auth R] MOL2 format, chain S [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain AA [auth I] mmCIF format, chain BA [auth J] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth L] mmCIF format, chain EA [auth M] mmCIF format, chain FA [auth N] mmCIF format, chain GA [auth O] mmCIF format, chain HA [auth P] mmCIF format, chain IA [auth Q] mmCIF format, chain JA [auth R] mmCIF format, chain S [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth H]	AA [auth I] BA [auth J] CA [auth K] DA [auth L] EA [auth M] AA [auth I], BA [auth J], CA [auth K], DA [auth L], EA [auth M], FA [auth N], GA [auth O], HA [auth P], IA [auth Q], JA [auth R], S [auth A], T [auth B], U [auth C], V [auth D], W [auth E], X [auth F], Y [auth G], Z [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain IA [auth Q] Focus chain JA [auth R] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth M] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain IA [auth Q] Focus chain JA [auth R] Focus chain S [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.282 (Depositor), 0.277 (DCC)
R-Value Work: 0.279 (Depositor), 0.276 (DCC)
R-Value Observed: 0.279 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.27	α = 90
b = 80.24	β = 106.5
c = 223.82	γ = 90

Software Package:

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

Structure Validation

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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, Refinement description