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PDBsum entry 2g4j
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protein metals links
Isomerase/metal-binding protein PDB id
2g4j

 

 

 

 

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Contents
Protein chain
386 a.a. *
Metals
_CL
_CA
_MG
Waters ×238
* Residue conservation analysis
PDB id:
2g4j
Name: Isomerase/metal-binding protein
Title: Anomalous substructure of glucose isomerase
Structure: Xylose isomerase. Chain: a. Ec: 5.3.1.5
Source: Streptomyces rubiginosus. Organism_taxid: 1929
Resolution:
1.85Å     R-factor:   0.153     R-free:   0.177
Authors: C.Mueller-Dieckmann,M.S.Weiss
Key ref:
C.Mueller-Dieckmann et al. (2007). On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Acta Crystallogr D Biol Crystallogr, 63, 366-380. PubMed id: 17327674 DOI: 10.1107/S0907444906055624
Date:
22-Feb-06     Release date:   20-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24300  (XYLA_STRRU) -  Xylose isomerase from Streptomyces rubiginosus
Seq:
Struc: 		388 a.a.
386 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.5  - xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: alpha-D-xylose = alpha-D-xylulofuranose
alpha-D-xylose
 = alpha-D-xylulofuranose
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1107/S0907444906055624 Acta Crystallogr D Biol Crystallogr 63:366-380 (2007)
PubMed id: 17327674  
 
 
On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, M.S.Weiss.
 
  ABSTRACT  
 
23 different crystal forms of 19 different biological macromolecules were examined with respect to their anomalously scattering substructures using diffraction data collected at a wavelength of 2.0 A (6.2 keV). In more than 90% of the cases the substructure was found to contain more than just the protein S atoms. The data presented suggest that chloride, sulfate, phosphate or metal ions from the buffer or even from the purification protocol are frequently bound to the protein molecule and that these ions are often overlooked, especially if they are not bound at full occupancy. Thus, in order to fully describe the macromolecule under study, it seems desirable that any structure determination be complemented with a long-wavelength data set.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Anomalous scattering length ( f''] ) values in units of electrons at = 1.0 Å (red) and = 2.0 Å (green) for elements 11-20 according to Cromer & Liberman (1970[Cromer, D. & Liberman, D. (1970). J. Chem. Phys. 53, 1891-1898.]).
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 366-380) copyright 2007.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460451 N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and R.A.de Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.
  Acta Crystallogr D Biol Crystallogr, 67, 331-337.  
21460452 R.J.Read, and A.J.McCoy (2011).
Using SAD data in Phaser.
  Acta Crystallogr D Biol Crystallogr, 67, 338-344.  
21525646 R.M.Leal, G.P.Bourenkov, O.Svensson, D.Spruce, M.Guijarro, and A.N.Popov (2011).
Experimental procedure for the characterization of radiation damage in macromolecular crystals.
  J Synchrotron Radiat, 18, 381-386.  
20382985 G.L.Taylor (2010).
Introduction to phasing.
  Acta Crystallogr D Biol Crystallogr, 66, 325-338.  
20724792 J.Gabadinho, A.Beteva, M.Guijarro, V.Rey-Bakaikoa, D.Spruce, M.W.Bowler, S.Brockhauser, D.Flot, E.J.Gordon, D.R.Hall, B.Lavault, A.A.McCarthy, J.McCarthy, E.Mitchell, S.Monaco, C.Mueller-Dieckmann, D.Nurizzo, R.B.Ravelli, X.Thibault, M.A.Walsh, G.A.Leonard, and S.M.McSweeney (2010).
MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments.
  J Synchrotron Radiat, 17, 700-707.  
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
  Acta Crystallogr D Biol Crystallogr, 66, 783-788.  
19219048 A.Guskov, J.Kern, A.Gabdulkhakov, M.Broser, A.Zouni, and W.Saenger (2009).
Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride.
  Nat Struct Mol Biol, 16, 334-342.
PDB codes: 3bz1 3bz2
19581484 B.Z.Wang, P.Guo, B.J.Hang, L.Li, J.He, and S.P.Li (2009).
Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp. strain JZ-1 and characterization of the gene product.
  Appl Environ Microbiol, 75, 5496-5500.  
  19255463 S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, and A.McPherson (2009).
High-resolution structure of proteinase K cocrystallized with digalacturonic acid.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 192-198.
PDB code: 3dyb
  18323597 C.Mueller-Dieckmann, S.Kernstock, J.Mueller-Dieckmann, M.S.Weiss, and F.Koch-Nolte (2008).
Structure of mouse ADP-ribosylhydrolase 3 (mARH3).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 156-162.
PDB code: 2qty
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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