6NLZ

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment degradation product B9D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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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 fragment degradation product 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KSP (Subject of Investigation/LOI)
Query on KSP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D]
[(1R,2S)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid
C14 H16 O4
LULBZYDRYZGRST-ZJUUUORDSA-N
KSJ (Subject of Investigation/LOI)
Query on KSJ

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
Q [auth D]
[(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid
C14 H16 O4
LULBZYDRYZGRST-VHSXEESVSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.61α = 90
b = 105.72β = 90
c = 154.53γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

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: 2020-01-15
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references