[English] 日本語
Yorodumi
- PDB-6y2v: Crystal structure of the double mutant L13R I16K of Low Molecular... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y2v
TitleCrystal structure of the double mutant L13R I16K of Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP)
ComponentsLow molecular weight phosphotyrosine protein phosphatase
KeywordsHYDROLASE / Engineered
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight, mammalian / : / 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
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLevy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Commonwealth Scholarship Commission (United Kingdom) United Kingdom
CitationJournal: Plos One / Year: 2020
Title: Computational and structure-guided design of phosphoinositide substrate specificity into the tyrosine specific LMW-PTP enzyme.
Authors: Egbe, E. / Levy, C.W. / Tabernero, L.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3073
Polymers18,0611
Non-polymers2452
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-5 kcal/mol
Surface area8040 Å2
Unit cell
Length a, b, c (Å)56.625, 41.287, 56.898
Angle α, β, γ (deg.)90.000, 91.809, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

-
Components

#1: Protein Low molecular weight phosphotyrosine protein phosphatase / LMW-PTPase / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase / Red ...LMW-PTPase / Adipocyte acid phosphatase / Low molecular weight cytosolic acid phosphatase / Red cell acid phosphatase 1


Mass: 18061.457 Da / Num. of mol.: 1 / Mutation: L13R I16K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris, 25% PEG3350, pH 5.5 / Temp details: Cold room

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→33.36 Å / Num. obs: 9025 / % possible obs: 99.04 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.34 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.062 / Net I/σ(I): 9.87
Reflection shellResolution: 2→2.072 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 917 / CC1/2: 0.718 / Rpim(I) all: 0.38 / % possible all: 99.78

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWW

1xww


Resolution: 2→33.36 Å / SU ML: 0.1666 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8789
RfactorNum. reflection% reflection
Rfree0.2313 480 5.33 %
Rwork0.1826 --
obs0.1851 8999 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.64 Å2
Refinement stepCycle: LAST / Resolution: 2→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 15 91 1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021274
X-RAY DIFFRACTIONf_angle_d0.47221717
X-RAY DIFFRACTIONf_chiral_restr0.0417185
X-RAY DIFFRACTIONf_plane_restr0.0025224
X-RAY DIFFRACTIONf_dihedral_angle_d22176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.280.271520.21812845X-RAY DIFFRACTION99.67
2.28-2.880.23051670.20342800X-RAY DIFFRACTION98.74
2.88-33.360.22061610.16362874X-RAY DIFFRACTION98.73
Refinement TLS params.Method: refined / Origin x: -14.7011401931 Å / Origin y: 0.816287854349 Å / Origin z: 14.4902950662 Å
111213212223313233
T0.143698803236 Å2-0.0216325822911 Å2-0.00639128211815 Å2-0.0926114316889 Å2-0.011848539913 Å2--0.149009215908 Å2
L2.40797055093 °20.110582959028 °20.0371187442019 °2-1.52087509212 °2-0.520301477122 °2--2.46340331247 °2
S-0.036966907399 Å °0.00779418956184 Å °0.122328057007 Å °-0.154587303733 Å °0.0494780387223 Å °-0.00841851569211 Å °0.0148800272328 Å °-0.163075767341 Å °-0.00266504562326 Å °
Refinement TLS groupSelection details: all

+
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