[English] 日本語
Yorodumi
- PDB-7n0z: Structure of PPM1H phosphatase with manganese ions at the active site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n0z
TitleStructure of PPM1H phosphatase with manganese ions at the active site
ComponentsProtein phosphatase 1H
KeywordsHYDROLASE
Function / homology
Function and homology information


[pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / glutamatergic synapse / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily
Similarity search - Domain/homology
: / Protein phosphatase 1H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKhan, A.R. / Waschbusch, D.
CitationJournal: Embo Rep. / Year: 2021
Title: Structural basis for the specificity of PPM1H phosphatase for Rab GTPases.
Authors: Waschbusch, D. / Berndsen, K. / Lis, P. / Knebel, A. / Lam, Y.P. / Alessi, D.R. / Khan, A.R.
History
DepositionMay 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein phosphatase 1H
B: Protein phosphatase 1H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,10210
Polymers100,7242
Non-polymers3788
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-57 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.779, 101.159, 148.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein phosphatase 1H


Mass: 50361.977 Da / Num. of mol.: 2 / Mutation: C56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPM1H, ARHCL1, KIAA1157, URCC2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ULR3, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 100mM Tris-Cl 15% reagent alcohol 10mM MnCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.19→63.93 Å / Num. obs: 365198 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.19-2.266.71.00741530.7550.4151.09193.6
9.31-63.9360.0378400.9980.0160.04199.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7l4j

7l4j


Resolution: 2.19→63.93 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 4703 4.55 %
Rwork0.1945 98751 -
obs0.1962 103454 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.87 Å2 / Biso mean: 57.0325 Å2 / Biso min: 31.69 Å2
Refinement stepCycle: final / Resolution: 2.19→63.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 8 211 6435
Biso mean--48.74 52.5 -
Num. residues----785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.220.37391060.29951991209760
2.22-2.240.27791590.280733453504100
2.24-2.270.3551570.281133563513100
2.27-2.30.31251590.284833583517100
2.3-2.330.30541600.26863385354599
2.33-2.360.33031610.280733763537100
2.36-2.40.31131560.273277343399
2.4-2.430.30791620.27433533515100
2.43-2.470.34781560.27973353350999
2.47-2.510.31941580.2643312347098
2.51-2.550.33361540.25863290344498
2.55-2.60.28151630.2443356351999
2.6-2.650.29391580.226733603518100
2.65-2.710.27821540.22443333348799
2.71-2.760.30971600.22153362352299
2.76-2.830.27831600.233351351199
2.83-2.90.26091630.219233523515100
2.9-2.980.25591560.22123347350399
2.98-3.060.30731610.24373355351699
3.06-3.160.24171660.22613353351999
3.16-3.280.29541550.21443279343499
3.28-3.410.21491620.19843337349999
3.41-3.560.23121600.1863301346198
3.56-3.750.21171550.17933325348098
3.75-3.990.21321600.17533315347599
3.99-4.290.18261570.14723317347499
4.29-4.730.16761630.14113378354199
4.73-5.410.18391530.15323296344999
5.41-6.810.23091610.18363309347098
6.81-63.930.16661480.16363329347799
Refinement TLS params.Method: refined / Origin x: -17.225 Å / Origin y: 10.8006 Å / Origin z: -21.3186 Å
111213212223313233
T0.3438 Å2-0.0185 Å2-0.0071 Å2-0.347 Å2-0.0103 Å2--0.4265 Å2
L0.386 °20.0254 °2-0.155 °2-0.4922 °20.239 °2--1.545 °2
S0.0195 Å °-0.0332 Å °0.0061 Å °-0.048 Å °-0.0608 Å °-0.028 Å °-0.035 Å °-0.0623 Å °0.0402 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 512
2X-RAY DIFFRACTION1allB34 - 513
3X-RAY DIFFRACTION1allC1 - 6
4X-RAY DIFFRACTION1allS2 - 223
5X-RAY DIFFRACTION1allD1 - 2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more