5V4D | pdb_00005v4d

Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfA from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb5V4D/pdb

Classification: Structural genomics, unknown function
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-09 Released: 2017-04-05
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Krishnan, A., Babnigg, G., Schneewind, O., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.180 (Depositor), 0.180 (DCC)
R-Value Work:
0.153 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (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

Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfA from Yersinia pestis

Kim, Y., Chhor, G., Endres, M., Krishnan, A., Babnigg, G., Schneewind, O., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 83.19 kDa
Atom Count: 6,710
Modeled Residue Count: 759
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative translational inhibitor protein	A, B, C, D, E A, B, C, D, E, F	128	Yersinia pestis	Mutation(s): 0 Gene Names: tdcF3, y3551, YP_2944, YPO0627
UniProt
Find proteins for A0A3N4B564 (Yersinia pestis) Explore A0A3N4B564 Go to UniProtKB: A0A3N4B564
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3N4B564
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain N [auth C] SDF format, chain I [auth A] MOL2 format, chain T [auth E] MOL2 format, chain N [auth C] MOL2 format, chain I [auth A] mmCIF format, chain T [auth E] mmCIF format, chain N [auth C] mmCIF format, chain I [auth A]	I [auth A], N [auth C], T [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth C] Focus chain T [auth E] Interactions & Density Focus chain I [auth A] Focus chain N [auth C] Focus chain T [auth E]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] M [auth C] O [auth D] P [auth D] G [auth A], J [auth B], M [auth C], O [auth D], P [auth D], Q [auth E], U [auth F]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain U [auth F]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] K [auth B] L [auth B] R [auth E] S [auth E] H [auth A], K [auth B], L [auth B], R [auth E], S [auth E], V [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth E] Focus chain S [auth E] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.180 (Depositor), 0.180 (DCC)
R-Value Work: 0.153 (Depositor), 0.153 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.927	α = 90
b = 80.919	β = 90
c = 141.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description