[English] 日本語
Yorodumi
- PDB-6h8r: CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h8r
TitleCRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 (STEP) IN COMPLEX WITH COMPOUND 2
ComponentsTyrosine-protein phosphatase non-receptor type 5
KeywordsHYDROLASE / PROTEIN PHOSPHATASE / PTN5 / STEP / ALLOSTERIC MODULATOR
Function / homology
Function and homology information


Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm ...Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-FWB / Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHoerer, S. / Fiegen, D. / Schnapp, G.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Allosteric Activation of Striatal-Enriched Protein Tyrosine Phosphatase (STEP, PTPN5) by a Fragment-like Molecule.
Authors: Tautermann, C.S. / Binder, F. / Buttner, F.H. / Eickmeier, C. / Fiegen, D. / Gross, U. / Grundl, M.A. / Heilker, R. / Hobson, S. / Hoerer, S. / Luippold, A. / Mack, V. / Montel, F. / Peters, ...Authors: Tautermann, C.S. / Binder, F. / Buttner, F.H. / Eickmeier, C. / Fiegen, D. / Gross, U. / Grundl, M.A. / Heilker, R. / Hobson, S. / Hoerer, S. / Luippold, A. / Mack, V. / Montel, F. / Peters, S. / Bhattacharya, S. / Vaidehi, N. / Schnapp, G. / Thamm, S. / Zeeb, M.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5203
Polymers35,2051
Non-polymers3152
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.095, 64.375, 100.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 5 / Neural-specific protein-tyrosine phosphatase / Striatum-enriched protein-tyrosine phosphatase / STEP


Mass: 35204.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN5 / Production host: Escherichia coli (E. coli) / References: UniProt: P54829, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FWB / 3-[(2~{S})-2-azanylpropyl]-5-(trifluoromethyl)phenol


Mass: 219.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12F3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24 % PEG 3350, 0.2 M ammonium sulfate and 0.1 M BIS-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.655→54.255 Å / Num. obs: 33135 / % possible obs: 79 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.22 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 10.3
Reflection shellResolution: 1.655→1.795 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.195 / Mean I/σ(I) obs: 1.4 / Rsym value: 1.195 / % possible all: 18.5

-
Processing

Software
NameVersionClassification
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
Cootmodel building
BUSTER2.11.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BIJ

2bij


Resolution: 1.66→39.69 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.239 985 2.97 %RANDOM
Rwork0.2 ---
obs0.201 33123 79.5 %-
Displacement parametersBiso mean: 25.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.8535 Å20 Å20 Å2
2---2.769 Å20 Å2
3----1.0845 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.66→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 20 377 2735
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082534HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d886SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes439HARMONIC5
X-RAY DIFFRACTIONt_it2534HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion16.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion326SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies14HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3162SEMIHARMONIC4
LS refinement shellResolution: 1.66→1.75 Å / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.2921 -2.81 %
Rwork0.2728 657 -
all0.2732 676 -
obs--11.69 %
Refinement TLS params.Method: refined / Origin x: -14.9433 Å / Origin y: -5.3528 Å / Origin z: 16.5225 Å
111213212223313233
T-0.0183 Å2-0.0016 Å2-0.0007 Å2--0.07 Å2-0.0139 Å2---0.0466 Å2
L0.35 °20.0563 °2-0.314 °2-0.8115 °20.1357 °2--1.4996 °2
S0.006 Å °-0.0213 Å °-0.0156 Å °-0.0133 Å °0.0171 Å °-0.1424 Å °-0.0588 Å °0.1837 Å °-0.0231 Å °
Refinement TLS groupSelection details: { A|* }

+
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