6BI4 | pdb_00006bi4

2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-dehydratase (rfbB) from Bacillus anthracis str. Ames in Complex with NAD.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 
    0.204 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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Literature

Structure of the Bacillus anthracis dTDP-l-rhamnose biosynthetic pathway enzyme: dTDP-alpha-d-glucose 4,6-dehydratase, RfbB.

Gokey, T., Halavaty, A.S., Minasov, G., Anderson, W.F., Kuhn, M.L.

(2018) J Struct Biol 202: 175-181

  • DOI: https://doi.org/10.1016/j.jsb.2018.01.006
  • Primary Citation Related Structures: 
    6BI4

  • PubMed Abstract: 

    Many bacteria require l-rhamnose as a key cell wall component. This sugar is transferred to the cell wall using an activated donor dTDP-l-rhamnose, which is produced by the dTDP-l-rhamnose biosynthetic pathway. We determined the crystal structure of the second enzyme of this pathway dTDP-α-d-glucose 4,6-dehydratase (RfbB) from Bacillus anthracis. Interestingly, RfbB only crystallized in the presence of the third enzyme of the pathway RfbC; however, RfbC was not present in the crystal. Our work represents the first complete structural characterization of the four proteins of this pathway in a single Gram-positive bacterium.

    • Organizational Affiliation: 
    • Department of Chemistry and Biochemistry, San Francisco State University, USA.

Macromolecule Content 

  • Total Structure Weight: 164.52 kDa 
  • Atom Count: 10,407 
  • Modeled Residue Count: 1,242 
  • Deposited Residue Count: 1,384 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
dTDP-glucose 4,6-dehydratase
A, B, C, D
346Bacillus anthracis str. AmesMutation(s): 0 
Gene Names: rfbB
EC: 4.2.1.46
UniProt
Find proteins for A0A6L7HMN5 (Bacillus anthracis)
Explore A0A6L7HMN5 
Go to UniProtKB:  A0A6L7HMN5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L7HMN5
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
E, F
2N/A
Glycosylation Resources
GlyTouCan: G05551OP
GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD


Download:Ideal Coordinates CCD File
H [auth A],
M [auth B],
R [auth C],
V [auth D]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
N [auth B]
O [auth B]
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NI

Query on NI


Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free:  0.204 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.557α = 90
b = 165.557β = 90
c = 292.121γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-01-27
    Changes: Database references, Structure summary
  • Version 2.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2023-11-15
    Changes: Data collection
  • Version 2.4: 2024-10-16
    Changes: Structure summary