6BI4

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

PDB DOI: https://doi.org/10.2210/pdb6BI4/pdb
Entry: 6BI4 supersedes: 4EGB

Classification: LYASE
Organism(s): Bacillus anthracis str. Ames
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-10-31 Released: 2017-11-08
Deposition Author(s): Halavaty, A.S., Kuhn, M., Shuvalova, L., Minasov, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.204
R-Value Work: 0.167
R-Value Observed: 0.169

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.4 of the entry. See complete history.

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

PubMed: 29331609 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.jsb.2018.01.006
Primary Citation of 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
Modelled Residue Count: 1,242
Deposited Residue Count: 1,384
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-glucose 4,6-dehydratase	A, B, C, D	346	Bacillus anthracis str. Ames	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L7HMN5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E, F	2		N/A	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	H [auth A], M [auth B], R [auth C], V [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain W [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth D]	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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	E, F	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.204
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: I 4 2 2
Diffraction Data: https://doi.org/10.18430/m36bi4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.557	α = 90
b = 165.557	β = 90
c = 292.121	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-11-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

This entry supersedes: 4EGB

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

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Help and Resources

6BI4

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2