3HD2 | pdb_00003hd2

Crystal structure of E. coli HPPK(Q50A) in complex with MgAMPCPP and pterin

• PDB DOI: https://doi.org/10.2210/pdb3HD2/pdb

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


• Deposited: 2009-05-06 Released: 2010-05-19 
• Deposition Author(s): Blaszczyk, J., Li, Y., Yan, H., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.188 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Role of loop coupling in enzymatic catalysis and conformational dynamics

Blaszczyk, J., Li, Y., 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)

Macromolecule Content 

• Total Structure Weight: 18.72 kDa 
• Atom Count: 1,796 
• Modeled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	A	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APC	D [auth A]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H18 N5 O12 P3 CAWZRIXWFRFUQB-IOSLPCCCSA-N
PE0	E [auth A]	PTERINE C6 H5 N5 O HNXQXTQTPAJEJL-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.188 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.48	α = 90
b = 52.87	β = 102.71
c = 36.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Blaszczyk, J., Li, Y., Yan, H., Ji, X.

Revision History  

• Version 1.0: 2010-05-19
  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