5CX4 | pdb_00005cx4

Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase

PDB DOI: https://doi.org/10.2210/pdb5CX4/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-07-28 Released: 2016-08-17
Deposition Author(s): Li, A.W.H., Hemmings, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 ?
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The Hydrolytic Positional Specificity Towards Phytic Acid of a Bacterial Multiple Inositol Polyphosphate Phosphatase

Li, A.W.H., Brearley, C.A., Hemmings, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 98.57 kDa
Atom Count: 6,901
Modelled Residue Count: 792
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
multiple inositol polyphosphate histidine phosphatase 1	A, B	426	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1 Gene Names: BT_4744 EC: 3.1.3.62 (UniProt), 3.1.3.80 (UniProt)
UniProt
Find proteins for Q89YI8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89YI8 Go to UniProtKB: Q89YI8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89YI8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 ?
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 52.8	α = 90
b = 119.64	β = 108.08
c = 76.08	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.