6GIZ

PURPLE ACID PHYTASE FROM WHEAT ISOFORM B2 - SUBSTRATE COMPLEX

PDB DOI: https://doi.org/10.2210/pdb6GIZ/pdb

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

Deposited: 2018-05-15 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.167
R-Value Work: 0.136
R-Value Observed: 0.138

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 61.27 kDa
Atom Count: 4,661
Modelled Residue Count: 504
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F6MIW5
Sequence Annotations Expand
Reference Sequence

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, C	2		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	N [auth A], O [auth A], P [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A]	Q [auth A], R [auth A], S [auth A], T [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	K [auth A], L [auth A], M [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth A]	AA [auth A] BA [auth A] U [auth A] V [auth A] W [auth A] AA [auth A], BA [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.167
R-Value Work: 0.136
R-Value Observed: 0.138
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.73	α = 90
b = 126.73	β = 90
c = 107.04	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Faba-Rodriguez, R.

Brearley, C.A.

Hemmings, A.M.

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

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2022-06-08
Changes: Advisory, Database references, Structure summary
Version 2.2: 2024-01-17
Changes: Data collection, Refinement description