[English] 日本語
Yorodumi
- PDB-6u83: OmpA-like domain of FopA1 from Francisella tularensis subsp. tula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u83
TitleOmpA-like domain of FopA1 from Francisella tularensis subsp. tularensis SCHU S4
ComponentsOuter membrane associated protein
KeywordsPEPTIDE BINDING PROTEIN / outer membrane associated protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
D-ALANINE / Outer membrane associated protein
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3566 Å
AuthorsMichalska, K. / Skarina, T. / Stogios, P.J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: OmpA-like domain of FopA1 from Francisella tularensis subsp. tularensis SCHU S4
Authors: Michalska, K. / Skarina, T. / Stogios, P.J. / Di Leo, R. / Savchenko, A. / Joachimiak, A.
History
DepositionSep 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3064
Polymers18,7411
Non-polymers5663
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint6 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.788, 134.971, 31.206
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Outer membrane associated protein / FopA1


Mass: 18740.809 Da / Num. of mol.: 1 / Fragment: OmpA-like domain (UNP residues 223-393)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: fopA1, FTT_0583 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Magic / References: UniProt: Q5NH85
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, cryoprotectant: paratone, SITTING DROP, TEMPERATURE 295K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 19, 2019 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 10225 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 55.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Net I/σ(I): 26.25
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.157 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 528 / CC1/2: 0.899 / % possible all: 99.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXdev_2947refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5U1H

5u1h


Resolution: 2.3566→43.5059 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 510 5.01 %
Rwork0.2075 --
obs0.2091 10170 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.21 Å2 / Biso mean: 82.0066 Å2 / Biso min: 43.62 Å2
Refinement stepCycle: final / Resolution: 2.3566→43.5059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 37 5 1222
Biso mean--73.86 61.41 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0070.061233
X-RAY DIFFRACTIONf_angle_d0.89210.9231654
X-RAY DIFFRACTIONf_dihedral_angle_d18.727179.983752
X-RAY DIFFRACTIONf_chiral_restr0.0470.137180
X-RAY DIFFRACTIONf_plane_restr0.0050.032212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3566-2.59370.41671160.3284233396
2.5937-2.96890.2941290.2754233798
2.9689-3.74020.25451210.2143244499
3.7402-43.50590.19971440.1777254699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.81112.2325-2.47518.9423-6.53864.8954-0.51270.50590.218-0.97110.5360.4543-0.2974-0.4979-0.03470.95550.0024-0.05940.55740.05730.461-19.319-10.0205-10.1588
25.01942.3266-0.84634.1241-1.46322.2057-0.0775-0.04210.18760.17710.0745-0.0133-0.0498-0.01-0.00460.99770.0544-0.05410.4018-0.02830.3127-19.7967-19.755-1.8824
30.25690.3424-0.7075.35-4.13584.07680.4197-0.5245-0.20040.6508-0.5077-0.22910.0341-0.4037-0.22671.1064-0.06090.02480.7593-0.06940.6695-13.5066-2.2006-14.3458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 260 through 282 )A260 - 282
2X-RAY DIFFRACTION2chain 'A' and (resid 283 through 393 )A283 - 393
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 259 )A240 - 259

+
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