4HEI | pdb_00004hei

2A X-RAY STRUCTURE OF HPF from VIBRIO CHOLERAE

PDB DOI: https://doi.org/10.2210/pdb4HEI/pdb
Entry: 4HEI supersedes: 4FYL

Classification: TRANSLATION
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Mutation(s): No

Deposited: 2012-10-03 Released: 2012-10-24
Deposition Author(s): De Bari, H., Berry, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.281 (Depositor), 0.272 (DCC)
R-Value Work:
0.262 (Depositor), 0.246 (DCC)
R-Value Observed:
0.262 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structure of Vibrio cholerae ribosome hibernation promoting factor.

De Bari, H., Berry, E.A.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 228-236

PubMed: 23519794 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309113000961
Primary Citation Related Structures:
4HEI

PubMed Abstract:
The X-ray crystal structure of ribosome hibernation promoting factor (HPF) from Vibrio cholerae is presented at 2.0 Å resolution. The crystal was phased by two-wavelength MAD using cocrystallized cobalt. The asymmetric unit contained two molecules of HPF linked by four Co atoms. The metal-binding sites observed in the crystal are probably not related to biological function. The structure of HPF has a typical β-α-β-β-β-α fold consistent with previous structures of YfiA and HPF from Escherichia coli. Comparison of the new structure with that of HPF from E. coli bound to the Thermus thermophilus ribosome [Polikanov et al. (2012), Science, 336, 915-918] shows that no significant structural changes are induced in HPF by binding.

Organizational Affiliation

Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Avenue, Syracuse, NY 13210, USA.

Macromolecule Content

Total Structure Weight: 22.95 kDa
Atom Count: 1,675
Modeled Residue Count: 183
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOME HIBERNATION PROTEIN YHBH	A, B	95	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0
UniProt
Find proteins for H9L4N9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore H9L4N9 Go to UniProtKB: H9L4N9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H9L4N9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3CO Query on 3CO Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain K [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], K [auth B], R [auth B]	COBALT (III) ION Co JAWGVVJVYSANRY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain R [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A] L [auth B] M [auth B] N [auth B] P [auth B] E [auth A], L [auth B], M [auth B], N [auth B], P [auth B], Q [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain Q [auth B]
UNL Query on UNL Download:Ideal Coordinates CCD File	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], S [auth B]	Unknown ligand ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.281 (Depositor), 0.272 (DCC)
R-Value Work: 0.262 (Depositor), 0.246 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.354	α = 90
b = 46.354	β = 90
c = 174.492	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-10-24

Deposition Author(s):

De Bari, H.

Berry, E.A.

This entry supersedes: 4FYL

Revision History (Full details and data files)

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2012-12-12
Changes: Derived calculations
Version 1.2: 2013-03-06
Changes: Database references, Derived calculations, Other
Version 1.3: 2013-05-22
Changes: Database references
Version 1.4: 2017-06-21
Changes: Database references, Source and taxonomy
Version 1.5: 2019-11-20
Changes: Derived calculations
Version 1.6: 2024-02-28
Changes: Data collection, Database references, Derived calculations