5CY4 | pdb_00005cy4

Crystal structure of an oligoribonuclease from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb5CY4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-07-30 Released: 2015-08-19
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.202 (Depositor), 0.204 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an oligoribonuclease from Acinetobacter baumannii

Lukacs, C.M., Fairman, J.W., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 139.43 kDa
Atom Count: 9,446
Modeled Residue Count: 1,089
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A, B, C, D, E A, B, C, D, E, F	196	Acinetobacter baumannii	Mutation(s): 0 Gene Names: orn, ABUW_3367, BL01_16870, IOMTU433_3284, IX87_17160, LH92_02780, MRSN16875_02860, RQ24_13780, RQ85_08810, RU84_15800... orn, ABUW_3367, BL01_16870, IOMTU433_3284, IX87_17160, LH92_02780, MRSN16875_02860, RQ24_13780, RQ85_08810, RU84_15800, VM83_02650, WH42_12930 EC: 3.1
UniProt
Find proteins for V5VGJ9 (Acinetobacter baumannii) Explore V5VGJ9 Go to UniProtKB: V5VGJ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V5VGJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain J [auth A] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain J [auth A] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	J [auth A], T [auth E], W [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain J [auth A] Focus chain T [auth E] Focus chain W [auth F]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth D], R [auth E], S [auth E], U [auth F], V [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.202 (Depositor), 0.204 (DCC)
R-Value Work: 0.169 (Depositor), 0.171 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.71	α = 90
b = 102.88	β = 90
c = 184.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-08-19

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-08-19
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.2: 2024-10-23
Changes: Structure summary