4XED

PKD domain of M14-like peptidase from Thermoplasmatales archaeon SCGC AB-540-F20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

PKD domain of M14-like peptidase from Thermoplasmatales archaeon SCGC AB-540-F20

Michalska, K.Joachimiak, G.Endres, M.Joachimiak, A.Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidase M14, carboxypeptidase AA99Thermoplasmatales archaeon SCGC AB-540-F20Mutation(s): 0 
Gene Names: MBGDF03_00742
Find proteins for M7U057 (Thermoplasmatales archaeon SCGC AB-540-F20)
Explore M7U057 
Go to UniProtKB:  M7U057
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.186α = 90
b = 48.869β = 90
c = 78.509γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000phasing
HKL-3000data scaling
SBC-Collectdata collection
SHELXphasing
MLPHAREphasing
DMphasing
ARPmodel building
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094585

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Advisory, Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence, Derived calculations