[English] 日本語
Yorodumi
- PDB-2luo: NMR solution structure of apo-MptpA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2luo
TitleNMR solution structure of apo-MptpA
ComponentsLOW MOLECULAR WEIGHT PROTEIN-TYROSINE-PHOSPHATASE A
KeywordsHYDROLASE / Low Molecular Weight Tyrosine Phosphatase / MptpA
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell endomembrane system / symbiont-mediated perturbation of host phagocytosis / : / Blockage of phagosome acidification / symbiont-mediated suppression of host apoptosis / Suppression of apoptosis / host cell cytoplasmic vesicle / Prevention of phagosomal-lysosomal fusion / protein dephosphorylation / protein-tyrosine-phosphatase ...symbiont-mediated perturbation of host cell endomembrane system / symbiont-mediated perturbation of host phagocytosis / : / Blockage of phagosome acidification / symbiont-mediated suppression of host apoptosis / Suppression of apoptosis / host cell cytoplasmic vesicle / Prevention of phagosomal-lysosomal fusion / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Modulation by Mtb of host immune system / host cell nucleus / extracellular region / plasma membrane / cytosol
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
Low molecular weight protein-tyrosine phosphatase A / Low molecular weight protein-tyrosine phosphatase A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, MOLECULAR DYNAMICS
AuthorsStehle, T. / Sreeramulu, S. / Loehr, F. / Richter, C. / Saxena, K. / Jonker, H.R.A. / Schwalbe, H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Apo-structure of the Low Molecular Weight Protein-tyrosine Phosphatase A (MptpA) from Mycobacterium tuberculosis Allows for Better Target-specific Drug Development.
Authors: Stehle, T. / Sreeramulu, S. / Lohr, F. / Richter, C. / Saxena, K. / Jonker, H.R. / Schwalbe, H.
History
DepositionJun 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LOW MOLECULAR WEIGHT PROTEIN-TYROSINE-PHOSPHATASE A


Theoretical massNumber of molelcules
Total (without water)17,9761
Polymers17,9761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein LOW MOLECULAR WEIGHT PROTEIN-TYROSINE-PHOSPHATASE A / PTPase


Mass: 17976.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Description: original pET16bTev vector was double NcoI/BlpId digested and cloned into the modified pKM263 (6xHis tag ProtGB1-TEV between Nde1 and Xho1) vector
Gene: ptpA, Rv2234, MT2293, MTCY427.15 / Plasmid: pKM263 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS
References: UniProt: P65716, UniProt: P9WIA1*PLUS, protein-tyrosine-phosphatase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: SORTED ON LOWEST ENERGY AFTER ARIA WATER REFINEMENT
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D (H)C(NC)H
1613D HCD(CG)CB-TOCSY
1713D (H)CC(CO)NH-TOCSY
1813D (H)CB(CG)CCH-TOCSY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
11123D 1H-15N NOESY
11222D (T1,T2,HetNOE) 1H-15N HSQC
11322D (IPAP) 1H-15N HSQC
11422D (IPAP) 1H-15N HSQC
11523D HNHA
NMR detailsText: SORTED ON LOWEST ENERGY AFTER ARIA WATER REFINEMENT

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] mptpa, 50 mM arginine / glutamine, 25 mM HEPES, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 15N] mptpa, 50 mM arginine / glutamine, 25 mM HEPES, 10 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMmptpa-1[U-100% 13C; U-100% 15N]1
50 mMarginine / glutamine-21
25 mMHEPES-31
10 mMDTT-41
1.0 mMmptpa-5[U-100% 15N]2
50 mMarginine / glutamine-62
25 mMHEPES-72
10 mMDTT-82
Sample conditionsIonic strength: 0 / pH: 7.0 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE6004

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
Sparky3.114Goddardpeak picking
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
CARA1.8.4.2Keller and Wuthrichdata analysis
CARA1.8.4.2Keller and Wuthrichpeak picking
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
CYANA3.9Guntert, Mumenthaler and Wuthrichrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, MOLECULAR DYNAMICS
Software ordinal: 1
Details: SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS, STRUCTURE DETERMINATION WITH AUTOMATED NOE ASSIGNMENT USING CYANA, FINAL STRUCTURE REFINEMENT IN EXPLICIT WATER WITH ADDITIONAL DIFFUSION ...Details: SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS, STRUCTURE DETERMINATION WITH AUTOMATED NOE ASSIGNMENT USING CYANA, FINAL STRUCTURE REFINEMENT IN EXPLICIT WATER WITH ADDITIONAL DIFFUSION ANISOTROPY DATA USING ARIA PROTOCOLS WITH CNS.
NMR constraintsNOE constraints total: 4821 / NOE intraresidue total count: 815 / NOE long range total count: 1611 / NOE medium range total count: 1103 / NOE sequential total count: 1292 / Hydrogen bond constraints total count: 138
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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