8IH6 | pdb_00008ih6

Crystal structure of decarboxylase-hydratase complex from Pseudomonas species AP-3

• PDB DOI: https://doi.org/10.2210/pdb8IH6/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-22 Released: 2024-02-28 
• Deposition Author(s): Shi, Q.L., Su, D.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of decarboxylase-hydratase complex from Pseudomonas species AP-3

Shi, Q.L., Su, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A5B5 Pseudo Symmetry: Dihedral - D5  (Explore in 3D)
Pseudo Stoichiometry: Homo 10-mer - A10 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 277.61 kDa 
• Atom Count: 19,701 
• Modeled Residue Count: 2,597 
• Deposited Residue Count: 2,620 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxopent-4-enoate hydratase	A, B, D [auth C], E [auth D], F [auth E]	266	Pseudomonas sp.	Mutation(s): 0  Gene Names: amnF EC: 4.2.1.80
UniProt
Find proteins for Q9KWS4 (Pseudomonas sp) Explore Q9KWS4  Go to UniProtKB:  Q9KWS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4-oxalocrotonate decarboxylase	C [auth F], G, H, I, J	258	Pseudomonas sp.	Mutation(s): 0  Gene Names: amnE EC: 4.1.1.77
UniProt
Find proteins for Q9KWS3 (Pseudomonas sp) Explore Q9KWS3  Go to UniProtKB:  Q9KWS3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	K [auth B], L [auth G], M [auth H], N [auth J]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.976	α = 90
b = 107.792	β = 124.46
c = 164.847	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Shi, Q.L., Su, D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2017YFA0505903

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release