[English] 日本語
Yorodumi
- PDB-7mom: Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypica... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mom
TitleCrystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) in complex with a metaphosphate intermediate
ComponentsTyrosine-protein phosphatase DSP1
KeywordsHYDROLASE / inositol / inositol pyrophosphate / TRANSFERASE / cell-signaling / phosphatase / substrate recognition / reaction mechanism / intermediate / phosphate / metaphosphate / molecular dynamic simulation / self-activation / catalytic water
Function / homology
Function and homology information


inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / diphosphoinositol-polyphosphate diphosphatase / phosphatase activity / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Atypical dual-specificity phosphatase Siw14-like, plant and fungi / Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PHOSPHITE ION / Inositol diphosphatase DSP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046-29 United States
CitationJournal: Nat Commun / Year: 2022
Title: A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop.
Authors: Wang, H. / Perera, L. / Jork, N. / Zong, G. / Riley, A.M. / Potter, B.V.L. / Jessen, H.J. / Shears, S.B.
History
DepositionMay 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase DSP1
B: Tyrosine-protein phosphatase DSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7107
Polymers39,3182
Non-polymers3925
Water7,674426
1
A: Tyrosine-protein phosphatase DSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8163
Polymers19,6591
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase DSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8944
Polymers19,6591
Non-polymers2353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.896, 124.896, 124.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-726-

HOH

21A-810-

HOH

31B-765-

HOH

41B-791-

HOH

51B-810-

HOH

61B-813-

HOH

-
Components

#1: Protein Tyrosine-protein phosphatase DSP1 / Protein PLANT AND FUNGI ATYPICAL DUAL-SPECIFICITY PHOSPHATASE 1 / AtPFA-DSP1 / Tyrosine-protein ...Protein PLANT AND FUNGI ATYPICAL DUAL-SPECIFICITY PHOSPHATASE 1 / AtPFA-DSP1 / Tyrosine-protein phosphatase At1g05000


Mass: 19658.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DSP1, PTP135, At1g05000, T7A14.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZVN4, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.4 M NaCl, 100mM HEPES pH7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 4.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% ...Details: 0.4 M NaCl, 100mM HEPES pH7.2, 50 mM beta-mercaptoethanol at 298K (3 ul of 4.5 mg/ml protein plus 1 ul of well buffer in the crystallization drop). The formed crystal was soaked in 30% PEG400, 13mM MgCl2, 33mM NaF, 50 mM beta-mercaptoethanol, 66 mM HEPES, pH 8.0, and 0.1 mM 5-InsP7 for 2 hours.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 71430 / % possible obs: 100 % / Redundancy: 10 % / Rrim(I) all: 0.06 / Net I/σ(I): 40.8
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3538 / Rrim(I) all: 0.969

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→39.53 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.25 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.141 3627 5.1 %RANDOM
Rwork0.1152 ---
obs0.1165 67721 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 334.54 Å2 / Biso mean: 20.385 Å2 / Biso min: 5.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.7→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 20 426 3123
Biso mean--35.77 41.7 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132894
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172700
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6383912
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5746293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68921.06151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3191521
X-RAY DIFFRACTIONr_chiral_restr0.0810.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023261
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02658
X-RAY DIFFRACTIONr_rigid_bond_restr1.85435594
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2 270 -
Rwork0.189 4887 -
obs--99.13 %

+
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