[English] 日本語
Yorodumi
- PDB-6dtm: Crystal Structure of Helicobacter pylori TlpA Chemoreceptor Ligan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dtm
TitleCrystal Structure of Helicobacter pylori TlpA Chemoreceptor Ligand Binding Domain
ComponentsMethyl-accepting chemotaxis protein TlpA
KeywordsSIGNALING PROTEIN / chemoreceptor / helix bundle / PAS/Cache
Function / homologyMethyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / signal transduction / membrane / metal ion binding / Methyl-accepting chemotaxis protein TlpA
Function and homology information
Biological speciesHelicobacter pylori SS1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRemington, S.J. / Guillemin, K. / Sweeney, E. / Perkins, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Protein Sci. / Year: 2018
Title: Structures of the ligand-binding domain of Helicobacter pylori chemoreceptor TlpA.
Authors: Sweeney, E.G. / Perkins, A. / Kallio, K. / James Remington, S. / Guillemin, K.
History
DepositionJun 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein TlpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5882
Polymers33,5531
Non-polymers351
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Presumed nonphysiological state
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area13170 Å2
Unit cell
Length a, b, c (Å)143.220, 67.830, 29.415
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-481-

HOH

-
Components

#1: Protein Methyl-accepting chemotaxis protein TlpA


Mass: 33552.719 Da / Num. of mol.: 1 / Fragment: periplasmic ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori SS1 (bacteria) / Gene: tlpA, HPYLSS1_00094 / Plasmid: pBH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1U9IS38
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: depends on crystal / PH range: 6, 6.5 or 7 depending on crystal

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Feb 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→29.3 Å / Num. obs: 16013 / % possible obs: 97.3 % / Redundancy: 7.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.049 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.788 / Rpim(I) all: 0.397 / % possible all: 91.3

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
SAINTdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.342 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.323 497 5.11 %
Rwork0.2221 --
obs0.2275 9724 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 1 84 2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181959
X-RAY DIFFRACTIONf_angle_d1.6472644
X-RAY DIFFRACTIONf_dihedral_angle_d17.7971212
X-RAY DIFFRACTIONf_chiral_restr0.072320
X-RAY DIFFRACTIONf_plane_restr0.009330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.75170.39161280.26032254X-RAY DIFFRACTION97
2.7517-3.14950.40461150.25382282X-RAY DIFFRACTION99
3.1495-3.96650.33141300.21952327X-RAY DIFFRACTION100
3.9665-29.34360.25181240.19512364X-RAY DIFFRACTION100

+
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