[English] 日本語
Yorodumi
- PDB-4acl: 3D Structure of DotU from Francisella novicida -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4acl
Title3D Structure of DotU from Francisella novicida
ComponentsTSSL
KeywordsPROTEIN TRANSPORT / T6SS / MICROBIAL SURFACE STRUCTURES / MEMBRANE PROTEIN / VIRULENCE FACTOR
Function / homologyType IV / VI secretion system, DotU / Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / : / Type IV / VI secretion system DotU domain-containing protein
Function and homology information
Biological speciesFRANCISELLA NOVICIDA (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.49 Å
AuthorsRobb, C.S. / Nano, F.E. / Boraston, A.B.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structure of the Conserved Type Six Secretion Protein Tssl (Dotu) from Francisella Novicida
Authors: Robb, C.S. / Nano, F.E. / Boraston, A.B.
History
DepositionDec 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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_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: TSSL
B: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,12817
Polymers48,6172
Non-polymers2,51115
Water72140
1
A: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,63710
Polymers24,3081
Non-polymers1,3299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TSSL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4907
Polymers24,3081
Non-polymers1,1826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.309, 85.314, 66.989
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TSSL


Mass: 24308.490 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 1-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FRANCISELLA NOVICIDA (bacteria) / Strain: U112 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0Q7H7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Au
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.25 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growpH: 8 / Details: 0.1 M TRIS, PH 8.8, 20% PEG 3350.

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2010 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→65.99 Å / Num. obs: 15228 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.1 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
d*TREKdata reduction
d*TREKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.49→65.43 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.962 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27867 754 5 %RANDOM
Rwork0.2181 ---
obs0.22117 14199 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.297 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20.17 Å2
2--2.55 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.49→65.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 21 40 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222635
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9633564
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.81624.851134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13315471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.42159
X-RAY DIFFRACTIONr_chiral_restr0.1270.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021977
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9011.51549
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68222503
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18331086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5094.51060
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.489→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 66 -
Rwork0.239 945 -
obs--91.08 %

+
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