5I47

Crystal structure of RimK domain protein ATP-grasp from Sphaerobacter thermophilus DSM 20745


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of RimK domain protein ATP-grasp from Sphaerobacter thermophilus DSM 20745

Chang, C.Duke, N.Wu, R.Clancy, S.Joachimiak, A.Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RimK domain protein ATP-grasp
A, B
277Sphaerobacter thermophilus (strain DSM 20745 / S 6022)Mutation(s): 0 
Find proteins for D1C6B4 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022))
Go to UniProtKB:  D1C6B4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.641α = 90.00
b = 64.819β = 90.00
c = 160.075γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-3000data reduction
PHENIXrefinement
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM115586

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations