1T8X | pdb_00001t8x

r106g kdo8ps with pep and a5p

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.197 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Effects of the Arg106==>Gly mutation on the catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase.

Xu, X., Wang, J., Kona, F., Divvela, P., Stemmler, T., Gatti, D.L.

To be published.

Macromolecule Content 

  • Total Structure Weight: 60.24 kDa 
  • Atom Count: 4,508 
  • Modeled Residue Count: 513 
  • Deposited Residue Count: 534 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase
A, B
267Aquifex aeolicusMutation(s): 1 
Gene Names: KDSA, AQ_085
EC: 2.5.1.55
UniProt
Find proteins for O66496 (Aquifex aeolicus (strain VF5))
Explore O66496 
Go to UniProtKB:  O66496
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66496
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A5P

Query on A5P


Download:Ideal Coordinates CCD File
E [auth A]ARABINOSE-5-PHOSPHATE
C5 H13 O8 P
VJDOAZKNBQCAGE-WDCZJNDASA-N
PEP

Query on PEP


Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]		PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
CD

Query on CD


Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]		CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
F [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.375α = 90
b = 84.375β = 90
c = 160.459γ = 120
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2005-06-14 
    • Deposition Author(s): Gatti, D.L.

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description