4P69

Acek (D477A) ICDH complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The phosphatase mechanism of bifunctional kinase/phosphatase AceK.

Wang, S.Shen, Q.Chen, G.Zheng, J.Tan, H.Jia, Z.

(2014) Chem Commun (Camb) 50: 14117-14120

  • DOI: 10.1039/c4cc05375c
  • Primary Citation of Related Structures:  
    4P69

  • PubMed Abstract: 
  • We have revealed that bifunctional AceK kinase/phosphatase utilizes a stepwise addition-elimination mechanism in its dephosphorylation reaction. This work explains how AceK enables opposite kinase and phosphatase activities with Asp477 and a single Mg(2+) ion ...

    We have revealed that bifunctional AceK kinase/phosphatase utilizes a stepwise addition-elimination mechanism in its dephosphorylation reaction. This work explains how AceK enables opposite kinase and phosphatase activities with Asp477 and a single Mg(2+) ion.


    Organizational Affiliation

    College of Chemistry, Beijing Normal University, Beijing, 100875, China. jimin_z@bnu.edu.cn hongwei.tan@bnu.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase kinase/phosphataseA, B568Escherichia coli O157:H7Mutation(s): 1 
Gene Names: aceKZ5602ECs4934
EC: 2.7.11.5 (PDB Primary Data), 3.1.3 (PDB Primary Data)
UniProt
Find proteins for Q8X607 (Escherichia coli O157:H7)
Explore Q8X607 
Go to UniProtKB:  Q8X607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X607
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP]C, D415Escherichia coli K-12Mutation(s): 0 
Gene Names: icdicdAicdEb1136JW1122
EC: 1.1.1.42
UniProt
Find proteins for P08200 (Escherichia coli (strain K12))
Explore P08200 
Go to UniProtKB:  P08200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08200
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMP
Query on AMP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.16α = 90
b = 198.16β = 90
c = 156.071γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.3: 2018-05-30
    Changes: Advisory, Data collection, Derived calculations, Source and taxonomy