[English] 日本語
Yorodumi
- PDB-5got: Crystal structure of SP-PTP, low molecular weight protein tyrosin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5got
TitleCrystal structure of SP-PTP, low molecular weight protein tyrosine phosphatase from Streptococcus pyogenes
ComponentsLow molecular weight phosphotyrosine phosphatase family protein
KeywordsHYDROLASE / SP-PTP / LMWPTP / Streptococcus pyogenes
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity
Similarity search - Function
: / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsKu, B. / Keum, C.W. / KIim, S.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of SP-PTP, a low molecular weight protein tyrosine phosphatase from Streptococcus pyogenes
Authors: Ku, B. / Keum, C.W. / Lee, H.S. / Yun, H.-Y. / Shin, H.-C. / Kim, B.Y. / Kim, S.J.
History
DepositionJul 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Low molecular weight phosphotyrosine phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1494
Polymers18,0421
Non-polymers1063
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-27 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.003, 58.003, 218.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Low molecular weight phosphotyrosine phosphatase family protein / Protein tyrosine phosphatase / SP-PTP


Mass: 18042.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: ptpA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0C6G2S1, UniProt: Q9A1Y0*PLUS, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 150 mM potassium thiocyanate, 100 mM Bis-Tris, 8% polyethylene glycol 3350, 2% D-sorbitol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 18189 / % possible obs: 98.5 % / Redundancy: 10.5 % / Net I/σ(I): 37.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→32.946 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1789 10 %
Rwork0.1963 --
obs0.2004 17897 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→32.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 3 161 1395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071261
X-RAY DIFFRACTIONf_angle_d0.861701
X-RAY DIFFRACTIONf_dihedral_angle_d14.159753
X-RAY DIFFRACTIONf_chiral_restr0.05180
X-RAY DIFFRACTIONf_plane_restr0.004215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9015-1.95290.34141330.311193X-RAY DIFFRACTION99
1.9529-2.01040.28951330.27221206X-RAY DIFFRACTION99
2.0104-2.07530.29971350.24441207X-RAY DIFFRACTION98
2.0753-2.14940.25181330.22991199X-RAY DIFFRACTION99
2.1494-2.23550.26761340.2141211X-RAY DIFFRACTION99
2.2355-2.33720.2481350.2141204X-RAY DIFFRACTION99
2.3372-2.46040.26691330.20461206X-RAY DIFFRACTION98
2.4604-2.61440.28931350.19721222X-RAY DIFFRACTION99
2.6144-2.81620.24041360.21721225X-RAY DIFFRACTION99
2.8162-3.09940.22611390.20811249X-RAY DIFFRACTION99
3.0994-3.54750.26721410.18311271X-RAY DIFFRACTION99
3.5475-4.46770.18491440.15761302X-RAY DIFFRACTION100
4.4677-32.95140.20721580.17741413X-RAY DIFFRACTION99

+
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