[English] 日本語
Yorodumi
- PDB-3wqa: Acinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wqa
TitleAcinetobacter sp. Tol 5 AtaA YDD-DALL3 domains in C-terminal stalk fused to GCN4 adaptors (CstalkC1ii)
ComponentsTrimeric autotransporter adhesin
KeywordsCELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber
Function / homology
Function and homology information


cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Trimeric autotransporter adhesin AtaA
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsKoiwai, K. / Hartmann, M.D. / Yoshimoto, S. / Nur 'Izzah, N. / Suzuki, A. / Linke, D. / Lupas, A.N. / Hori, K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Toughness and Flexibility in the C-terminal Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin.
Authors: Koiwai, K. / Hartmann, M.D. / Linke, D. / Lupas, A.N. / Hori, K.
History
DepositionJan 24, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Trimeric autotransporter adhesin
B: Trimeric autotransporter adhesin
C: Trimeric autotransporter adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5087
Polymers67,2243
Non-polymers2844
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27970 Å2
ΔGint-226 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.110, 43.680, 95.564
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Trimeric autotransporter adhesin


Mass: 22408.002 Da / Num. of mol.: 3 / Fragment: UNP residues 3334-3474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter (bacteria) / Strain: Tol 5 / Gene: ataA / Plasmid: pIBA-GCN4tri / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: K7ZP88
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 67mM MES, 0.67M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→88.56 Å / Num. all: 26029 / Num. obs: 26029 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.39 Å2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.540.7730.6411.8313461418340490.76596.8
2.54-2.720.9060.4212.8113427393439280.599.8
2.72-2.930.930.3014.212328369436760.35999.5
2.93-3.210.950.2076.3110796339333790.24999.6
3.21-3.590.9790.139.9710788309930880.15499.6
3.59-4.140.9880.09412.589001272927020.11399
4.14-5.050.9960.06514.847270234923190.07898.7
5.05-7.080.9970.06514.896095183318130.07898.9
7.080.9950.04818.533249110210750.05897.5

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YO2

2yo2


Resolution: 2.401→38.322 Å / FOM work R set: 0.7472 / SU ML: 0.41 / σ(F): 1.37 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1199 4.94 %RANDOM
Rwork0.2133 ---
obs0.2179 24248 92.39 %-
all-24248 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.1 Å2 / Biso mean: 26.68 Å2 / Biso min: 2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.401→38.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 12 272 4829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084629
X-RAY DIFFRACTIONf_angle_d1.0896262
X-RAY DIFFRACTIONf_chiral_restr0.075752
X-RAY DIFFRACTIONf_plane_restr0.004827
X-RAY DIFFRACTIONf_dihedral_angle_d17.1411730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4006-2.49670.39621300.2842451258190
2.4967-2.61030.34461370.25292634277196
2.6103-2.74790.3571360.24162621275795
2.7479-2.920.30281340.21982624275895
2.92-3.14540.38061270.22682507263492
3.1454-3.46170.28681350.20272576271193
3.4617-3.96220.30151420.19192606274893
3.9622-4.99020.25921260.18192473259989
4.9902-38.32690.27651320.21612557268988

+
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