5H6O

Porphobilinogen deaminase from Vibrio Cholerae

• PDB DOI: https://doi.org/10.2210/pdb5H6O/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-11-14 Released: 2017-11-15 
• Deposition Author(s): Funamizu, T., Chen, M., Tanaka, Y., Ishimori, K., Uchida, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Porphobilinogen deaminase from Vibrio Cholerae

Funamizu, T., Chen, M., Tanaka, Y., Ishimori, K., Uchida, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.08 kDa 
• Atom Count: 2,191 
• Modelled Residue Count: 281 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Porphobilinogen deaminase	A	317	Vibrio cholerae	Mutation(s): 0  Gene Names: hemC, ERS013197_03721 EC: 2.5.1.61
UniProt
Find proteins for Q9KVM1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVM1  Go to UniProtKB:  Q9KVM1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPM	B [auth A]	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid C20 H24 N2 O8 LCAXMKQKEYTFDM-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.23	α = 90
b = 94.23	β = 90
c = 165.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Funamizu, T., Chen, M., Tanaka, Y., Ishimori, K., Uchida, T.

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description