[English] 日本語
Yorodumi
- PDB-4lrq: Crystal structure of a Low Molecular Weight Phosphotyrosine phosp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lrq
TitleCrystal structure of a Low Molecular Weight Phosphotyrosine phosphatase from Vibrio choleraeO395
ComponentsPhosphotyrosine protein phosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / 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 / Protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNath, S. / Banerjee, R. / Sen, U.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family.
Authors: Nath, S. / Banerjee, R. / Sen, U.
History
DepositionJul 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: 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 / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphotyrosine protein phosphatase
B: Phosphotyrosine protein phosphatase
C: Phosphotyrosine protein phosphatase
D: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,85616
Polymers69,2504
Non-polymers1,60612
Water7,062392
1
A: Phosphotyrosine protein phosphatase
C: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4288
Polymers34,6252
Non-polymers8036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-55 kcal/mol
Surface area14110 Å2
MethodPISA
2
B: Phosphotyrosine protein phosphatase
D: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4288
Polymers34,6252
Non-polymers8036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-58 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 87.470, 73.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
Phosphotyrosine protein phosphatase


Mass: 17312.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: VC0395_A0559, VC395_1055 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: A5F2Q3, UniProt: A0A0H3ALA8*PLUS, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.4M ammonium sulfate, 0.1M citric acid pH 5.0, 2% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2011
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.284
11-K, -H, -L20.21
11K, H, -L30.216
11-h,-k,l40.29
ReflectionResolution: 1.45→23.89 Å / Num. obs: 110187 / % possible obs: 98.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.45→1.488 Å / Mean I/σ(I) obs: 7.8 / Num. unique all: 110187 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERMRphasing
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→23.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.214 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16063 5518 5 %RANDOM
Rwork0.15159 ---
obs0.15204 104633 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.062 Å2
Refine analyzeLuzzati coordinate error free: 0.011 Å
Refinement stepCycle: LAST / Resolution: 1.45→23.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 92 392 5129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194820
X-RAY DIFFRACTIONr_bond_other_d0.0010.024602
X-RAY DIFFRACTIONr_angle_refined_deg0.9591.9886496
X-RAY DIFFRACTIONr_angle_other_deg0.939310633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4175593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81824.537227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92515850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8271532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021051
X-RAY DIFFRACTIONr_rigid_bond_restr2.90234820
X-RAY DIFFRACTIONr_sphericity_free3.5565121
X-RAY DIFFRACTIONr_sphericity_bonded5.0255014
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 432 -
Rwork0.399 7459 -
obs--95.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.70.02930.04481.50240.16921.4318-0.00420.0020.0451-0.02490.01680.0432-0.013-0.0419-0.01260.02590.00980.00230.02370.00660.0375-10.5685-21.3912-19.0189
21.1383-0.4379-0.1641.05180.30871.28840.02240.02810.0009-0.0335-0.0110.05790.0005-0.0462-0.01140.0031-0.0059-0.00370.02240.00730.0263-30.55595.4556-7.0247
31.02110.52270.02851.7176-0.17941.27450.0436-0.11290.01560.2374-0.05070.075-0.0511-0.02240.00710.0447-0.01390.00790.0233-0.0010.0267-14.8796-43.44623.8284
41.3623-0.80980.11191.580.17171.4468-0.0841-0.1644-0.04660.18350.07270.028-0.0121-0.01440.01150.04650.00740.0030.0210.010.0336-13.5927-9.367816.0302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 149
2X-RAY DIFFRACTION2B2 - 150
3X-RAY DIFFRACTION3C1 - 149
4X-RAY DIFFRACTION4D1 - 148

+
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