1SNN

3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate.

Steinbacher, S.Schiffmann, S.Bacher, A.Fischer, M.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1338-1340

  • DOI: https://doi.org/10.1107/S0907444904009862
  • Primary Citation of Related Structures:  
    1SNN

  • PubMed Abstract: 

    The crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal centre has recently been determined at 1.7 A resolution. The enzyme converts ribulose 5-phosphate into 3,4-dihydroxy-2-butanone 4-phosphate, while its C4 atom is released as formate. The resulting four-carbon body supplies all eight C atoms for the xylene moiety of riboflavin. Three of the four hydroxyl groups of ribulose 5-phosphate were coordinated by the metal ions. Based on crystallographic refinement, the metals were assigned as zinc and calcium, which were present in the crystallization buffer. Neither metal supports the enzymatic reaction. In the present study, the correctness of this assignment is assessed using anomalous diffraction data collected at the high-energy side of the zinc absorption edge (lambda = 1.2823 A). Only the three tentative zinc ions give strong peaks in an anomalous difference Fourier map (>20sigma), whereas the four tentative calcium ions do not show anomalous signals above the noise level. These results confirm the initial assignment. In addition, the resolution was improved to 1.55 A.


  • Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. steinbac@caltech.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3,4-dihydroxy-2-butanone 4-phosphate synthase
A, B
227Methanocaldococcus jannaschiiMutation(s): 1 
Gene Names: MJ0055
EC: 5.4.99 (PDB Primary Data), 4.1.99.12 (UniProt)
UniProt
Find proteins for Q60364 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q60364 
Go to UniProtKB:  Q60364
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60364
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5RP
Query on 5RP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
RIBULOSE-5-PHOSPHATE
C5 H11 O8 P
FNZLKVNUWIIPSJ-UHNVWZDZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
H [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.395α = 90
b = 69.366β = 93.58
c = 57.574γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description