5V4D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative translational inhibitor protein
A, B, C, D, E
A, B, C, D, E, F
128Yersinia pestisMutation(s): 0 
Gene Names: tdcF3y3551YP_2944YPO0627
UniProt
Find proteins for A0A3N4B564 (Yersinia pestis)
Explore A0A3N4B564 
Go to UniProtKB:  A0A3N4B564
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3N4B564
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
N [auth C],
T [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
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
CA
Query on CA

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.927α = 90
b = 80.919β = 90
c = 141.929γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited 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