3AJX | pdb_00003ajx

Crystal Structure of 3-Hexulose-6-Phosphate Synthase

• PDB DOI: https://doi.org/10.2210/pdb3AJX/pdb

• Classification: LYASE
• Organism(s): Mycobacterium gastri
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-06-24 Released: 2010-11-03 
• Deposition Author(s): Kita, A., Orita, I., Yurimoto, H., Kato, N., Sakai, Y., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 3-hexulose-6-phosphate synthase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily

Orita, I., Kita, A., Yurimoto, H., Kato, N., Sakai, Y., Miki, K.

(2010) Proteins 78: 3488-3492

• PubMed: 20938979 
• DOI: https://doi.org/10.1002/prot.22860
• Primary Citation Related Structures: 
  3AJX

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Organizational Affiliation: 
• Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 84.42 kDa 
• Atom Count: 6,796 
• Modeled Residue Count: 828 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hexulose-6-phosphate synthase	A, B, C, D	207	Mycobacterium gastri	Mutation(s): 1  Gene Names: rmpA EC: 4.1.2.43
UniProt
Find proteins for Q9LBW4 (Mycobacterium gastri) Explore Q9LBW4  Go to UniProtKB:  Q9LBW4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], I [auth B], M [auth C], O [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	E [auth A], J [auth C], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], H [auth B], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.043	α = 90
b = 57.354	β = 90.69
c = 113.623	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Kita, A., Orita, I., Yurimoto, H., Kato, N., Sakai, Y., Miki, K.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-22
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description