6GJ9 | pdb_00006gj9

PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - REGENERATION COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb6GJ9/pdb

• Classification: HYDROLASE
• Organism(s): Triticum aestivum
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2018-05-16 Released: 2019-11-27 
• Deposition Author(s): Faba-Rodriguez, R., Brearley, C.A., Hemmings, A.M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.196 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a cereal purple acid phytase provides insights to phytate degradation in plants

Faba-Rodriguez, R., Dionisio, G., Brinch-Pedersen, H., Brearley, C.A., Hemmings, A.M.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.68 kDa 
• Atom Count: 4,821 
• Modeled Residue Count: 504 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purple acid phosphatase	A	516	Triticum aestivum	Mutation(s): 0  Gene Names: PAPhy EC: 3.1.3.2
UniProt
Find proteins for F6MIW5 (Triticum aestivum) Explore F6MIW5  Go to UniProtKB:  F6MIW5
Glycosylation
Glycosylation Sites: 6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	M [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	K [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.196 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.971	α = 90
b = 126.971	β = 90
c = 107.518	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-27 
Deposition Author(s): Faba-Rodriguez, R., Brearley, C.A., Hemmings, A.M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M022978/1

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary