6NDR

Crystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC from Legionella pneumophila Philadelphia 1 in complex with dTDP-4-KETO-L-RHAMNOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC from Legionella pneumophila Philadelphia 1 in complex with dTDP-4-KETO-L-RHAMNOSE

Abendroth, J.Schulze, M.-S.Mayclin, S.J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
dTDP-4-dehydrorhamnose 3,5-epimerase
A, B
195Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg0756
EC: 5.1.3.13
UniProt
Find proteins for Q5ZXH5 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZXH5 
Go to UniProtKB:  Q5ZXH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZXH5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TDO (Subject of Investigation/LOI)
Query on TDO

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
DTDP-4-KETO-L-RHAMNOSE
C16 H24 N2 O15 P2
PSXWNITXWWECNY-LPVGZGSHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
I [auth A]
K [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.38α = 90
b = 46.16β = 112.29
c = 102.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
MoRDaphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description