5J7M

Crystal structure of Cupin 2 conserved barrel domain protein from Kribbella flavida DSM 17836


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Cupin 2 conserved barrel domain protein from Kribbella flavida DSM 17836

Chang, C.Cuff, M.Chhor, G.Endres, M.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cupin 2 conserved barrel domain protein
A, B
123Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)Mutation(s): 0 
Find proteins for D2Q1L0 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399))
Go to UniProtKB:  D2Q1L0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A, B
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-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: 2.07 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 61.162α = 90.00
b = 61.162β = 90.00
c = 120.973γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-3000data reduction
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: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references, Structure summary
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations