[English] 日本語
Yorodumi
- PDB-3wi5: Crystal structure of the Loop 7 mutant PorB from Neisseria mening... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wi5
TitleCrystal structure of the Loop 7 mutant PorB from Neisseria meningitidis serogroup B
ComponentsMajor outer membrane protein P.IB
KeywordsMEMBRANE PROTEIN / beta-barrel / porin / outer membrane
Function / homology
Function and homology information


Toll Like Receptor TLR1:TLR2 Cascade / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / ER-Phagosome pathway
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Major outer membrane protein P.IB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKattner, C. / Toussi, D. / Wetzler, L.M. / Ruppel, N. / Massari, P. / Tanabe, M.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognition.
Authors: Kattner, C. / Toussi, D.N. / Zaucha, J. / Wetzler, L.M. / Ruppel, N. / Zachariae, U. / Massari, P. / Tanabe, M.
History
DepositionSep 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Major outer membrane protein P.IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2043
Polymers33,8251
Non-polymers3782
Water1,47782
1
A: Major outer membrane protein P.IB
hetero molecules

A: Major outer membrane protein P.IB
hetero molecules

A: Major outer membrane protein P.IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6119
Polymers101,4763
Non-polymers1,1356
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8410 Å2
ΔGint-57 kcal/mol
Surface area42070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.486, 143.486, 178.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Major outer membrane protein P.IB / PIB / Protein IB / Class 3 protein / Porin


Mass: 33825.363 Da / Num. of mol.: 1 / Mutation: D259A, D260K, E266R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: porB, NMB2039 / Production host: Escherichia coli (E. coli) / References: UniProt: P30690
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 65mM HEPES pH 7.5, 1.1M tri-sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2012
RadiationMonochromator: toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25466 / % possible obs: 92.2 % / Observed criterion σ(F): 17.4 / Observed criterion σ(I): 1.55
Reflection shellResolution: 2.4→2.45 Å / % possible all: 73

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VZT

3vzt


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25596 1791 7 %RANDOM
Rwork0.22745 ---
obs0.22946 23673 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.113 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0.57 Å2-0 Å2
2---1.15 Å2-0 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 26 82 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192465
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9353330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2524.298121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61515392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2031514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021927
LS refinement shellResolution: 2.404→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 107 -
Rwork0.305 1376 -
obs--72.27 %

+
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