3HSD | pdb_00003hsd

Crystal structure of E. coli HPPK(Y53A)

• PDB DOI: https://doi.org/10.2210/pdb3HSD/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-06-10 Released: 2010-06-23 
• Deposition Author(s): Blaszczyk, J., Li, Y., Yan, H., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Pterin-binding site mutation Y53A, N55A or F123A and activity of E. coli HPPK.

Li, Y., Blaszczyk, J., Ji, X., Yan, H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.44 kDa 
• Atom Count: 3,059 
• Modeled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HPPK	A, B	158	Escherichia coli K-12	Mutation(s): 1  Gene Names: b0142, foIK, folK, JW0138 EC: 2.7.6.3
UniProt
Find proteins for P26281 (Escherichia coli (strain K12)) Explore P26281  Go to UniProtKB:  P26281

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A], I [auth A], J [auth A], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	F [auth A], G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.04	α = 90
b = 47.47	β = 108.89
c = 72.53	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Blaszczyk, J., Li, Y., Yan, H., Ji, X.

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2023-09-06
  Changes: Refinement description