2WM8 | pdb_00002wm8

Crystal structure of human magnesium-dependent phosphatase 1 of the haloacid dehalogenase superfamily (MGC5987)

PDB DOI: https://doi.org/10.2210/pdb2WM8/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-06-30 Released: 2009-07-28
Deposition Author(s): Yue, W.W., Shafqat, N., Pike, A.C.W., Chaikuad, A., Bray, J.E., Pilka, E.W., Burgess-Brown, N., Hapka, E., Filippakopoulos, P., von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.198 (Depositor), 0.210 (DCC)
R-Value Work:
0.163 (Depositor), 0.177 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Human Magnesium-Dependent Phosphatase 1 of the Haloacid Dehalogenase Superfamily (Mgc5987)

Yue, W.W., Shafqat, N., Pike, A.C.W., Chaikuad, A., Bray, J.E., Filippakopoulos, P., von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 21.52 kDa
Atom Count: 1,681
Modeled Residue Count: 170
Deposited Residue Count: 187
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAGNESIUM-DEPENDENT PHOSPHATASE 1	A	187	Homo sapiens	Mutation(s): 0 EC: 3.8.1 (PDB Primary Data), 3.1.3 (UniProt), 3.1.3.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86V88 (Homo sapiens) Explore Q86V88 Go to UniProtKB: Q86V88
PHAROS: Q86V88 GTEx: ENSG00000213920
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86V88
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.198 (Depositor), 0.210 (DCC)
R-Value Work: 0.163 (Depositor), 0.177 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.34	α = 90
b = 62.34	β = 90
c = 111.86	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description