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PDBsum entry 1b6g

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protein ligands metals links
Hydrolase PDB id
1b6g
Jmol
Contents
Protein chain
310 a.a. *
Ligands
SO4
GOL ×7
Metals
_CL ×2
Waters ×601
* Residue conservation analysis
PDB id:
1b6g
Name: Hydrolase
Title: Haloalkane dehalogenase at ph 5.0 containing chloride
Structure: Haloalkane dehalogenase. Chain: a. Engineered: yes
Source: Xanthobacter autotrophicus. Organism_taxid: 280. Strain: gj10. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.15Å     R-factor:   0.105     R-free:   0.145
Authors: I.S.Ridder,H.J.Rozeboom,B.W.Dijkstra
Key ref:
I.S.Ridder et al. (1999). Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 A resolution. Acta Crystallogr D Biol Crystallogr, 55, 1273-1290. PubMed id: 10393294 DOI: 10.1107/S090744499900534X
Date:
14-Jan-99     Release date:   13-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22643  (DHLA_XANAU) -  Haloalkane dehalogenase
Seq:
Struc:
310 a.a.
310 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.8.1.5  - Haloalkane dehalogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 1-haloalkane + H2O = a primary alcohol + halide
1-haloalkane
+ H(2)O
= primary alcohol
+ halide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to toxin   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S090744499900534X Acta Crystallogr D Biol Crystallogr 55:1273-1290 (1999)
PubMed id: 10393294  
 
 
Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 A resolution.
I.S.Ridder, H.J.Rozeboom, B.W.Dijkstra.
 
  ABSTRACT  
 
Crystals of the 35 kDa protein haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 diffract to 1.15 A resolution at cryogenic temperature using synchrotron radiation. Blocked anisotropic least-squares refinement with SHELXL gave a final conventional R factor of 10.51% for all reflections in the 15-1.15 A resolution range. The estimated r.m.s. errors of the model are 0.026 and 0.038 A for protein atoms and all atoms, respectively. The structure comprises all 310 amino acids, with 28 side chains and two peptide bonds in multiple conformations, two covalently linked Pb atoms, 601 water molecules, seven glycerol molecules, one sulfate ion and two chloride ions. Water molecules accounting for alternative solvent structure are modelled with a fixed occupancy of 0.5. The structure is described in detail and compared with previously reported dehalogenase structures refined at 1.9-2.3 A resolution. An analysis of the protein's geometry and stereochemistry reveals eight mean values of bond lengths and angles which deviate significantly from the Engh & Huber parameters, a wide spread in the main-chain omega torsion angle around its ideal value of 180 (6) degrees and a role for C-HcO interactions in satisfying the hydrogen-bond acceptor capacity of main-chain carbonyl O atoms in the central beta-sheet.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 2mF[o] - DF[c] electron density contoured at 0.82 e Å^-3 (1.5 , cyan) and 2.45 e Å^-3 (4.5 , dark blue) levels for (a) Trp194, (b) the peptide bond between Asn14 and Leu15, showing the two alternative main-chain conformations, (c) residue Arg112 as an example of a double side-chain conformation, also showing the partially occupied sulfate ion and two partially occupied water molecules, Wat547 and Wat581, and (d) a glycerol molecule. In (c) and (d), the low contouring levels are 0.55 e Å^-3 (1.0 ) and 0.68 e Å^-3 (1.25 ), respectively. Hydrogen bonds are depicted as dashed lines. This figure and Fig. 5-were generated with BOBSCRIPT (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 133-138.]).
Figure 5.
Figure 5 2mF[o] - DF[c] electron density contoured at 0.82 e Å^-3 (1.5 , cyan) and 2.45 e Å^-3 (4.5 , dark blue) levels for (a) the catalytic triad Asp124-His289-Asp260, illustrating the anisotropy around the Asp124 OD1 atom (stereoview); (b) the chloride ion, Wat197 and Wat518 in the active site plus surrounding residues (stereoview); (c) the Pb atom (purple) bound to Cys150 SG, also showing the neighbouring Met152 in two conformations, (d) the same for Cys233 SG with the neighbouring Phe99 residue. In the latter two panels the anomalous difference electron density is also displayed, contoured at +0.15 e Å^-3 (+8.0 , green) and -0.15 e Å^-3 (-8.0 , brown) and at +0.06 e Å^-3 (+3.0 , green) and -0.06 e Å^-3 (-3.0 , brown) levels for (c) and (d), respectively. In (c) especially, the orbitals of the electrons in the L shell can clearly be discriminated in the shape of the anomalous difference density.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 1273-1290) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21347487 J.Perry, K.Koteva, and G.Wright (2011).
Receptor domains of two-component signal transduction systems.
  Mol Biosyst, 7, 1388-1398.  
16085827 Y.Sato, M.Monincová, R.Chaloupková, Z.Prokop, Y.Ohtsubo, K.Minamisawa, M.Tsuda, J.Damborsky, and Y.Nagata (2005).
Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities.
  Appl Environ Microbiol, 71, 4372-4379.  
14675549 A.Vrielink, and N.Sampson (2003).
Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
  Curr Opin Struct Biol, 13, 709-715.  
12220491 B.Klaholz, and D.Moras (2002).
C-H...O hydrogen bonds in the nuclear receptor RARgamma--a potential tool for drug selectivity.
  Structure, 10, 1197-1204.
PDB code: 1fd0
11937643 M.G.Pikkemaat, and D.B.Janssen (2002).
Generating segmental mutations in haloalkane dehalogenase: a novel part in the directed evolution toolbox.
  Nucleic Acids Res, 30, E35-E35.  
10975456 A.W.Munro, P.Taylor, and M.D.Walkinshaw (2000).
Structures of redox enzymes.
  Curr Opin Biotechnol, 11, 369-376.  
10521454 I.S.Ridder, H.J.Rozeboom, K.H.Kalk, and B.W.Dijkstra (1999).
Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase.
  J Biol Chem, 274, 30672-30678.
PDB codes: 1qq5 1qq6 1qq7
10607665 M.Nardini, and B.W.Dijkstra (1999).
Alpha/beta hydrolase fold enzymes: the family keeps growing.
  Curr Opin Struct Biol, 9, 732-737.  
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 code is shown on the right.