3KIP

Crystal structure of type-II 3-dehydroquinase from C. albicans

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


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


Literature

Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions.

Trapani, S., Schoehn, G., Navaza, J., Abergel, C.

(2010) Acta Crystallogr D Biol Crystallogr 66: 514-521

  • DOI: https://doi.org/10.1107/S0907444910002763
  • Primary Citation of Related Structures:  
    3KIP

  • PubMed Abstract: 

    The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme from Candida albicans (approximately 190 kDa) and that of the orthologous Streptomyces coelicolor protein.

    • Organizational Affiliation: 

    Université de Montpellier 1, Montpellier, France. stefano.trapani@cbs.cnrs.fr


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-dehydroquinase, type II
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
167Candida albicansMutation(s): 0 
Gene Names: DQD1, DHQ99, CaO19.9823
EC: 4.2.1.10
UniProt
Find proteins for Q59Z17 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore Q59Z17 
Go to UniProtKB:  Q59Z17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59Z17
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS
Download Ideal Coordinates CCD File 
AA [auth A]
CB [auth W]
EA [auth D]
IA [auth G]
MA [auth J]
AA [auth A],
CB [auth W],
EA [auth D],
IA [auth G],
MA [auth J],
QA [auth N],
TA [auth P],
YA [auth T]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AB [auth V]
BA [auth B]
BB [auth W]
CA [auth C]
DA [auth D]
AB [auth V],
BA [auth B],
BB [auth W],
CA [auth C],
DA [auth D],
DB [auth X],
FA [auth E],
GA [auth F],
HA [auth G],
JA [auth H],
KA [auth I],
LA [auth J],
NA [auth K],
OA [auth M],
PA [auth N],
RA [auth O],
SA [auth P],
UA [auth Q],
VA [auth R],
WA [auth S],
XA [auth T],
Y [auth A],
Z [auth A],
ZA [auth U]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.103α = 90
b = 308.11β = 90
c = 97.152γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description