6NN0

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and fragment degradation product B9D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and B9D

Thompson, A.P.Polyak, S.W.Wegener, K.L.Bruning, J.B.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent dethiobiotin synthetase BioD
A, B, C, D
233Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: bioDRv1570MTCY336.33c
EC: 6.3.3.3
UniProt
Find proteins for P9WPQ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPQ5 
Go to UniProtKB:  P9WPQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPQ5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KSP
Query on KSP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C],
U [auth D]
[(1R,2S)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid
C14 H16 O4
LULBZYDRYZGRST-ZJUUUORDSA-N
KSJ
Query on KSJ

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
T [auth D]
[(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid
C14 H16 O4
LULBZYDRYZGRST-VHSXEESVSA-N
CTN
Query on CTN

Download Ideal Coordinates CCD File 
J [auth B],
S [auth D]
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
H [auth B]
I [auth B]
M [auth C]
N [auth C]
E [auth A],
H [auth B],
I [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.49α = 90
b = 106.56β = 90
c = 154.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1068885

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references