4CHI | pdb_00004chi

(R)-selective amine transaminase from Aspergillus fumigatus at 1.27 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 
    0.127 (Depositor), 0.127 (DCC) 
  • R-Value Work: 
    0.103 (Depositor), 0.103 (DCC) 
  • R-Value Observed: 
    0.104 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4CHI

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystallographic Characterization of the (R)-Selective Amine Transaminase from Aspergillus Fumigatus.

Thomsen, M.Skalden, L.Palm, G.J.Hohne, M.Bornscheuer, U.T.Hinrichs, W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1086

  • DOI: https://doi.org/10.1107/S1399004714001084
  • Primary Citation Related Structures: 
    4CHI

  • PubMed Abstract: 

    The importance of amine transaminases for producing optically pure chiral precursors for pharmaceuticals and chemicals has substantially increased in recent years. The X-ray crystal structure of the (R)-selective amine transaminase from the fungus Aspergillus fumigatus was solved by S-SAD phasing to 1.84 Å resolution. The refined structure at 1.27 Å resolution provides detailed knowledge about the molecular basis of substrate recognition and conversion to facilitate protein-engineering approaches. The protein forms a homodimer and belongs to fold class IV of the pyridoxal-5'-phosphate-dependent enzymes. Both subunits contribute residues to form two active sites. The structure of the holoenzyme shows the catalytically important cofactor pyridoxal-5'-phosphate bound as an internal aldimine with the catalytically responsible amino-acid residue Lys179, as well as in its free form. A long N-terminal helix is an important feature for the stability of this fungal (R)-selective amine transaminase, but is missing in branched-chain amino-acid aminotransferases and D-amino-acid aminotransferases.


  • Organizational Affiliation
    • Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany.

Macromolecule Content 

  • Total Structure Weight: 75.6 kDa 
  • Atom Count: 7,037 
  • Modeled Residue Count: 639 
  • Deposited Residue Count: 664 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
A, B
332Aspergillus fumigatus Af293Mutation(s): 0 
EC: 2.6.1 (PDB Primary Data), 2.6.1.18 (PDB Primary Data)
UniProt
Find proteins for Q4WH08 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q4WH08 
Go to UniProtKB:  Q4WH08
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4WH08
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP

Query on PLP



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
O [auth B],
P [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
Q [auth B],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free:  0.127 (Depositor), 0.127 (DCC) 
  • R-Value Work:  0.103 (Depositor), 0.103 (DCC) 
  • R-Value Observed: 0.104 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.367α = 90
b = 120.935β = 90
c = 135.464γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXCDEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Data collection
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary