[English] 日本語
Yorodumi
- PDB-6hqc: Structural investigation of the TasA anchoring protein TapA from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hqc
TitleStructural investigation of the TasA anchoring protein TapA from Bacillus subtilis
ComponentsTasA anchoring/assembly protein
KeywordsPROTEIN FIBRIL / TasA / TapA / anchoring / biofilm
Function / homologybacterial biofilm matrix / TasA anchoring/assembly protein / Signal peptide, camelysin / extracellular region / TasA anchoring/assembly protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.28 Å
AuthorsRoske, Y. / Heinemann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: TapA acts as specific chaperone in TasA filament formation by strand complementation.
Authors: Roske, Y. / Lindemann, F. / Diehl, A. / Cremer, N. / Higman, V.A. / Schlegel, B. / Leidert, M. / Driller, K. / Turgay, K. / Schmieder, P. / Heinemann, U. / Oschkinat, H.
History
DepositionSep 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TasA anchoring/assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4405
Polymers13,1921
Non-polymers2484
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint9 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.103, 61.135, 34.291
Angle α, β, γ (deg.)90.00, 106.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TasA anchoring/assembly protein / Biofilm assembly accessory protein TapA


Mass: 13192.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tapA, yqhD, yqxM, BSU24640 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 T7 Express / References: UniProt: P40949
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 20% PEG MME 550, 0.1M NaCl, 0.1M Bicine pH 9.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841, 0.9795
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
20.97951
ReflectionResolution: 1.28→32.8 Å / Num. obs: 30250 / % possible obs: 98.4 % / Redundancy: 4.44 % / Biso Wilson estimate: 26.69 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.0045 / Net I/σ(I): 14.19
Reflection shellResolution: 1.28→1.39 Å / Mean I/σ(I) obs: 0.85 / CC1/2: 0.432 / Rrim(I) all: 0.177 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.28→32.8 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.691 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19715 1513 5 %RANDOM
Rwork0.14718 ---
obs0.14969 28736 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.03 Å2
2--0.59 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.28→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 16 213 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02980
X-RAY DIFFRACTIONr_bond_other_d0.0040.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9681312
X-RAY DIFFRACTIONr_angle_other_deg0.9532193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47625.6141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27715189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.19152
X-RAY DIFFRACTIONr_chiral_restr0.1330.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021047
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4752.329469
X-RAY DIFFRACTIONr_mcbond_other2.4742.326468
X-RAY DIFFRACTIONr_mcangle_it3.0083.509586
X-RAY DIFFRACTIONr_mcangle_other3.0073.513587
X-RAY DIFFRACTIONr_scbond_it3.0062.755511
X-RAY DIFFRACTIONr_scbond_other3.0042.754511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.553.909724
X-RAY DIFFRACTIONr_long_range_B_refined5.30131.5351145
X-RAY DIFFRACTIONr_long_range_B_other5.29931.5471146
X-RAY DIFFRACTIONr_rigid_bond_restr2.18931913
X-RAY DIFFRACTIONr_sphericity_free29.3695123
X-RAY DIFFRACTIONr_sphericity_bonded11.41251981
LS refinement shellResolution: 1.279→1.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 109 -
Rwork0.387 2077 -
obs--95.67 %

+
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