7K6W

Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus in complex with myo-inositol hexakisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure of the PTP-like myo-inositol phosphatase from Desulfovibrio magneticus in complex with myo-inositol hexakisphosphate

Cleland, C.P.Van Herk, P.H.Mosimann, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myo-inositol phosphohydrolase
A, B, C, D
310Solidesulfovibrio magneticusMutation(s): 1 
Gene Names: DMR_16880
UniProt
Find proteins for C4XPJ9 (Solidesulfovibrio magneticus (strain ATCC 700980 / DSM 13731 / RS-1))
Explore C4XPJ9 
Go to UniProtKB:  C4XPJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4XPJ9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C],
U [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth B]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
S [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.839α = 90
b = 95.989β = 92.09
c = 103.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 2.0: 2021-11-24
    Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Refinement description