4H3U

Crystal structure of hypothetical protein with ketosteroid isomerase-like protein fold from Catenulispora acidiphila DSM 44928


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural characterization of a hypothetical protein: a potential agent involved in trimethylamine metabolism in Catenulispora acidiphila.

Filippova, E.V.Luan, C.H.Dunne, S.F.Kiryukhina, O.Minasov, G.Shuvalova, L.Anderson, W.F.

(2014) J Struct Funct Genomics 15: 33-40

  • DOI: https://doi.org/10.1007/s10969-014-9176-z
  • Primary Citation of Related Structures:  
    4H3U, 4HVN

  • PubMed Abstract: 

    Catenulispora acidiphila is a newly identified lineage of actinomycetes that produces antimicrobial activities and represents a promising source of novel antibiotics and secondary metabolites. Among the discovered protein coding genes, 68 % were assigned a putative function, while the remaining 32 % are genes encoding "hypothetical" proteins. Caci_0382 is one of the "hypothetical" proteins that has very few homologs. Sequence analysis shows that the protein belongs to the NTF2-like protein family. The structure of Caci_0382 demonstrates that it shares the same fold and has a similar active site as limonene-1,2-epoxide hydrolase, which suggests that it may have a related function. Using a fluorescence thermal shift assay, we identified stabilizing compounds that suggest potential natural ligands of Caci_0382. Using this information, we determined the crystal structure in complex with trimethylamine to provide a better understanding of the function of this uncharacterized protein.


  • Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry, Northwestern Feinberg School of Medicine, Chicago, IL, 60611, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein
A, B
158Catenulispora acidiphila DSM 44928Mutation(s): 0 
Gene Names: Caci_0382
UniProt
Find proteins for C7PVH9 (Catenulispora acidiphila (strain DSM 44928 / JCM 14897 / NBRC 102108 / NRRL B-24433 / ID139908))
Explore C7PVH9 
Go to UniProtKB:  C7PVH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7PVH9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
O [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
O [auth B],
P [auth B],
Q [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A],
T [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth B],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: P 61
  • Diffraction Data: https://doi.org/10.18430/M34H3U
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.578α = 90
b = 61.578β = 90
c = 144.576γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2014-04-23
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary