[English] 日本語
Yorodumi
- PDB-7mhw: Crystal structure of the protease inhibitor U-Omp19 from Brucella... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mhw
TitleCrystal structure of the protease inhibitor U-Omp19 from Brucella abortus fused to Maltose-binding protein
ComponentsMaltose/maltodextrin-binding periplasmic protein,Outer membrane lipoprotein omp19
KeywordsMEMBRANE PROTEIN / Protease inhibitor / MBP-fusion protein
Function / homology
Function and homology information


endopeptidase inhibitor activity / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex ...endopeptidase inhibitor activity / detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Outer membrane lipoprotein, Omp19, bacterial / Alkaline proteinase inhibitor/ Outer membrane lipoprotein Omp19 / Protease inhibitor Inh / Protease inhibitor, beta-barrel domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Outer membrane lipoprotein omp19
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Brucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDarriba, M.L. / Klinke, S. / Otero, L.H. / Cerutti, M.L. / Cassataro, J. / Pasquevich, K.A.
Funding support Argentina, United States, 4items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2017-1849 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT-2014-1250 Argentina
Bill & Melinda Gates FoundationOPP1060394 United States
Bill & Melinda Gates FoundationOPP1119024 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: A disordered region retains the full protease inhibitor activity and the capacity to induce CD8 + T cells in vivo of the oral vaccine adjuvant U-Omp19.
Authors: Laura Darriba, M. / Castro, C.P. / Coria, L.M. / Bruno, L. / Laura Cerutti, M. / Otero, L.H. / Chemes, L.B. / Rasia, R.M. / Klinke, S. / Cassataro, J. / Pasquevich, K.A.
History
DepositionApr 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Outer membrane lipoprotein omp19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4078
Polymers51,7341
Non-polymers6727
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-70 kcal/mol
Surface area21190 Å2
Unit cell
Length a, b, c (Å)141.670, 141.670, 132.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-202-

SO4

31A-334-

HOH

-
Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Outer membrane lipoprotein omp19


Mass: 51734.242 Da / Num. of mol.: 1 / Mutation: D(-233)A,K(-232)A,K(-76)A,E44A,K47A,D48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Brucella abortus (bacteria)
Gene: malE, b4034, JW3994, omp19, BAB1_1930 / Plasmid: pMAL-c2 / Strain: 2308
Details (production host): Maltose-binding protein fusion, cytoplasmic expression
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEX9, UniProt: Q2YLR6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsAll six substitutions are in the MBP. No mutations are in the OMP19 portion of the construct.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 62 % / Description: Bipyramids
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M ammonium sulfate, 0.1 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2018 / Details: KIRKPATRICK-BAEZ PAIR OF BIMORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.55→48.33 Å / Num. obs: 22227 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 67.24 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Net I/σ(I): 16.2
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2675 / CC1/2: 0.55 / Rpim(I) all: 0.575 / Rrim(I) all: 1.928 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MxCuBEdata collection
XDSdata reduction
PHENIXphasing
Cootmodel building
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LLS

1lls


Resolution: 2.55→48.33 Å / SU ML: 0.3624 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 27.4339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242 1048 5 %
Rwork0.2066 39802 -
obs0.2083 22203 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.76 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 35 37 3647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343689
X-RAY DIFFRACTIONf_angle_d0.63895019
X-RAY DIFFRACTIONf_chiral_restr0.0398543
X-RAY DIFFRACTIONf_plane_restr0.0033648
X-RAY DIFFRACTIONf_dihedral_angle_d5.5159496
LS refinement shellResolution: 2.55→2.61 Å
RfactorNum. reflection% reflection
Rfree0.3607 80 -
Rwork0.3347 1316 -
obs--99.86 %

+
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