4WU3 | pdb_00004wu3

Structure of the PTP-like myo-inositol phosphatase from Mitsuokella multacida in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate

PDB DOI: https://doi.org/10.2210/pdb4WU3/pdb

Classification: HYDROLASE
Organism(s): Mitsuokella multacida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-10-30 Released: 2015-12-09
Deposition Author(s): Bruder, L.M., Mosimann, S.C.
Funding Organization(s): Canada Foundation for Innovation, Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.221 (DCC)
R-Value Work:
0.190 (Depositor), 0.195 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol-(1,3,4,5)-tetrakisphosphate

Bruder, L.M.

To be published.

Macromolecule Content

Total Structure Weight: 294.47 kDa
Atom Count: 21,756
Modeled Residue Count: 2,360
Deposited Residue Count: 2,528
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYO-INOSITOL PHOSPHOHYDROLASE	A, B, C, D	632	Mitsuokella multacida	Mutation(s): 2 Gene Names: phyA EC: 3.1.3.8
UniProt
Find proteins for A3QMF6 (Mitsuokella multacida) Explore A3QMF6 Go to UniProtKB: A3QMF6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3QMF6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4IP Query on 4IP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D]	E [auth A] F [auth A] K [auth B] Q [auth C] R [auth C] E [auth A], F [auth A], K [auth B], Q [auth C], R [auth C], W [auth D]	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C₆ H₁₆ O₁₈ P₄ CIPFCGZLFXVXBG-CNWJWELYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	G [auth A] L [auth B] M [auth B] S [auth C] X [auth D] G [auth A], L [auth B], M [auth B], S [auth C], X [auth D], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain I [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain I [auth A]	AA [auth D] BA [auth D] H [auth A] I [auth A] J [auth A] AA [auth D], BA [auth D], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], T [auth C], U [auth C], V [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.213 (Depositor), 0.221 (DCC)
R-Value Work: 0.190 (Depositor), 0.195 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.899	α = 107.27
b = 86.68	β = 91.69
c = 124.149	γ = 90.01

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
Aimless	data scaling
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-12-09

Deposition Author(s):

Bruder, L.M.

Mosimann, S.C.

Funding Organization	Location	Grant Number
Canada Foundation for Innovation	Canada	--
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2015-12-09
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2020-01-08
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description