[English] 日本語
Yorodumi
- PDB-5z3m: Crystal structure of Low Molecular Weight Phosphotyrosine phospha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z3m
TitleCrystal structure of Low Molecular Weight Phosphotyrosine phosphatase (VcLMWPTP-2) from Vibrio choleraeO395
ComponentsPhosphotyrosine protein phosphatase
KeywordsHYDROLASE / Phosphatase / Ligand Bound
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 speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChatterjee, S. / Nath, S. / Sen, U.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Vibrio cholerae LMWPTP-2 display unique surface charge and grooves around the active site: Indicative of distinctive substrate specificity and scope to design specific inhibitor.
Authors: Chatterjee, S. / Nath, S. / Ghosh, B. / Sen, U.
History
DepositionJan 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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: Phosphotyrosine protein phosphatase
B: Phosphotyrosine protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,49341
Polymers37,6592
Non-polymers3,83439
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-22 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.912, 51.867, 83.896
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-406-

HOH

-
Components

#1: Protein Phosphotyrosine protein phosphatase


Mass: 18829.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A0440 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H3AM12, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: AMS, HEPES, GLYCEROL, MOPS, NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→19.402 Å / Num. obs: 31285 / % possible obs: 98.88 % / Redundancy: 2.53 % / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.692 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LRQ

4lrq


Resolution: 2.6→19.402 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 34.62
RfactorNum. reflection% reflection
Rfree0.2883 1570 5.02 %
Rwork0.2518 --
obs0.2538 31285 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 246 257 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052673
X-RAY DIFFRACTIONf_angle_d1.0613550
X-RAY DIFFRACTIONf_dihedral_angle_d22.7641033
X-RAY DIFFRACTIONf_chiral_restr0.038376
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.68380.34071470.2972671X-RAY DIFFRACTION100
2.6838-2.77950.35891460.28032749X-RAY DIFFRACTION100
2.7795-2.89040.28051400.28662770X-RAY DIFFRACTION100
2.8904-3.02150.3741300.27752658X-RAY DIFFRACTION98
3.0215-3.18010.38821240.29042699X-RAY DIFFRACTION98
3.1801-3.37840.27561320.25252709X-RAY DIFFRACTION99
3.3784-3.63770.28311340.23092739X-RAY DIFFRACTION99
3.6377-4.00080.22721350.22532755X-RAY DIFFRACTION99
4.0008-4.57310.28081680.21742661X-RAY DIFFRACTION99
4.5731-5.73690.27051760.24872674X-RAY DIFFRACTION99
5.7369-19.40290.26931380.25572630X-RAY DIFFRACTION97
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)
10.58190.5217-0.21841.50290.04431.3597-0.2013-0.044-0.2040.13440.0249-0.15350.29060.18570.03750.68490.07540.3007-0.0531-0.11810.152-26.35521.006713.7231
20.39960.2152-0.11220.6622-0.81951.0849-0.03740.0243-0.0852-0.1569-0.0083-0.04150.1811-0.01850.01980.7065-0.11080.20710.14280.02510.1571-40.2559-2.715413.8624
30.1654-0.5287-0.62363.90575.1256.7784-0.0853-0.0346-0.04940.2830.3434-0.16130.49340.7596-0.22770.60210.11720.28650.2147-0.0270.2925-30.7296-8.704214.9251
40.86071.50840.16313.4740.30690.07-0.053-0.0698-0.10760.2760.0401-0.00760.10080.0523-0.07480.64330.02830.26230.1834-0.04850.2512-32.059713.32318.8441
50.6828-0.0772-0.35160.97630.20340.2088-0.03450.1092-0.0606-0.1618-0.00880.0013-0.0510.0092-0.10030.6727-0.01220.15750.07460.0050.1158-30.832711.42827.2908
61.44080.7715-0.25663.1185-2.94363.7688-0.0083-0.02410.00320.0218-0.1539-0.1703-0.23490.20860.08130.59240.0310.19560.10310.03230.1537-29.391620.630110.8744
71.4868-0.32280.7622.68650.97271.6601-0.18880.2361-0.0106-0.0714-0.0538-0.08280.1851-0.00880.13890.822-0.07680.25710.1854-0.0010.2747-32.55463.44890.2576
81.0317-1.0186-1.09221.39131.25622.993-0.0368-0.1440.1660.08510.2432-0.2228-0.17720.3995-0.31920.61070.02450.36550.0912-0.12740.1389-24.6294-1.44453.8915
91.3193-0.2061-0.2740.95210.8314.0887-0.0548-0.0010.0731-0.03650.2138-0.1516-0.25260.5096-0.25380.5883-0.01110.28840.1563-0.11210.0832-32.8233-12.085131.6379
100.5013-0.1151-0.34881.26730.14380.74520.1236-0.09770.11620.12050.0406-0.057-0.06980.1058-0.13730.8723-0.04020.37520.1732-0.0280.2721-33.7187-13.304526.5335
110.0636-0.0502-0.03820.40350.62721.00370.036-0.03970.05050.00940.0010.056-0.0146-0.07650.07760.6382-0.07090.3470.1203-0.10410.2564-38.1126-3.086129.2958
121.3844-0.99830.7723.6749-1.17160.60480.0020.09620.3263-0.3192-0.0695-0.4402-0.0340.05880.03910.8057-0.0240.26970.1603-0.03260.4511-30.9566-24.033923.3
130.54941.3449-0.20064.0508-1.7332.10210.03960.24510.1734-0.05260.0467-0.0747-0.05640.0674-0.03470.7712-0.0010.24650.2006-0.00050.2749-33.2977-21.959934.7112
140.4166-0.5422-0.03312.8362-0.40940.1925-0.0363-0.00360.00780.1886-0.035-0.14770.10950.03490.0830.7368-0.00570.2830.06960.080.1993-33.6065-27.729234.6298
152.3446-1.0902-0.11443.17480.12522.2810.0812-0.19430.0330.01170.21870.0978-0.437-0.4787-0.2761.04250.03250.4210.320.03320.4393-45.2469-15.289739.7967
160.99280.3094-0.30613.1637-0.73812.5662-0.0186-0.07610.01680.06940.0075-0.18040.52490.1180.16061.0166-0.04340.32470.169-0.02460.2665-34.7197-10.639140.6209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 96 )
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 130 )
8X-RAY DIFFRACTION8chain 'A' and (resid 131 through 157 )
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 54 )
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 82 )
13X-RAY DIFFRACTION13chain 'B' and (resid 83 through 91 )
14X-RAY DIFFRACTION14chain 'B' and (resid 92 through 115 )
15X-RAY DIFFRACTION15chain 'B' and (resid 116 through 130 )
16X-RAY DIFFRACTION16chain 'B' and (resid 131 through 156 )

+
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://pdbjlc1.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