6DIN | pdb_00006din

High resolutionstructure of apo dTDP-4-dehydrorhamnose 3,5-epimerase

• PDB DOI: https://doi.org/10.2210/pdb6DIN/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-23 Released: 2018-05-30 
• Deposition Author(s): Chang, C., Jedrzejczak, R., Chhor, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

High resolutionstructure of apo dTDP-4-dehydrorhamnose 3,5-epimerase

Chang, C., Jedrzejczak, R., Chhor, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.54 kDa 
• Atom Count: 1,798 
• Modeled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose 3,5-epimerase	A	184	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: rmlC, rfbC, CAZ03_15755, HV91_29470, PAERUG_E15_London_28_01_14_02405, RW109_RW109_06764 EC: 5.1.3.13
UniProt
Find proteins for A0A0D6IV69 (Pseudomonas aeruginosa) Explore A0A0D6IV69  Go to UniProtKB:  A0A0D6IV69

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.854	α = 90
b = 58.854	β = 90
c = 160.908	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Chang, C., Jedrzejczak, R., Chhor, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary