3WGQ | pdb_00003wgq

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with DAP of from Clostridium tetani E88

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted APIClick on this verticalbar to view details

This is version 2.0 of the entry. See complete history. 


Literature

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with DAP of from Clostridium tetani E88

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meso-diaminopimelate dehydrogenase
A, B
326Clostridium tetani E88Mutation(s): 6 
Gene Names: CTC_02532, meso-dapdh
EC: 1.4.1.16
UniProt
Find proteins for Q890V3 (Clostridium tetani (strain Massachusetts / E88))
Explore Q890V3 
Go to UniProtKB:  Q890V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ890V3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
API
Query on API
Download Ideal Coordinates CCD File 
C [auth A]2,6-DIAMINOPIMELIC ACID
C7 H14 N2 O4
GMKMEZVLHJARHF-SYDPRGILSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.917α = 90
b = 135.702β = 110.43
c = 60.479γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted APIClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection