[English] 日本語
Yorodumi
- PDB-4lsh: Ion selectivity of OmpF porin soaked in 0.2M KBr -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lsh
TitleIon selectivity of OmpF porin soaked in 0.2M KBr
ComponentsOuter membrane protein F
KeywordsTRANSPORT PROTEIN / porin / outer membrane protein / beta-barrel / ion transport
Function / homology
Function and homology information


colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity / lipid binding / membrane / identical protein binding
Similarity search - Function
Porin, gammaproteobacterial / 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
BROMIDE ION / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBalasundaresan, D. / Blachowicz, L. / Roux, B.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.
Authors: Dhakshnamoorthy, B. / Ziervogel, B.K. / Blachowicz, L. / Roux, B.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 20, 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_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Outer membrane protein F
B: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,32615
Polymers74,3432
Non-polymers98313
Water5,855325
1
A: Outer membrane protein F
hetero molecules

A: Outer membrane protein F
hetero molecules

A: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,02524
Polymers111,5143
Non-polymers1,51121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11210 Å2
ΔGint-59 kcal/mol
Surface area41220 Å2
MethodPISA
2
B: Outer membrane protein F
hetero molecules

B: Outer membrane protein F
hetero molecules

B: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,95221
Polymers111,5143
Non-polymers1,43818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11570 Å2
ΔGint-62 kcal/mol
Surface area40680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.981, 116.981, 51.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 1 - 340 / Label seq-ID: 2 - 341

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Outer membrane protein F / Outer membrane protein 1A / Outer membrane protein B / Outer membrane protein IA / Porin OmpF


Mass: 37171.301 Da / Num. of mol.: 2 / Fragment: UNP residues 23-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0929, cmlB, coa, cry, JW0912, ompF, tolF / Plasmid: PPR272 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P02931
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, crystals soaked in 0.2 M potassium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.91956 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91956 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40073 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.44
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OMF

2omf


Resolution: 2.2→45.89 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.238 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.32 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29322 2011 5 %RANDOM
Rwork0.24479 ---
obs0.24732 38062 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.751 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-1.46 Å20 Å2
2---1.46 Å2-0 Å2
3---4.74 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5153 0 13 325 5491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025257
X-RAY DIFFRACTIONr_bond_other_d0.0030.024665
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9317106
X-RAY DIFFRACTIONr_angle_other_deg0.961310665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2065663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10924.93284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53215780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6031522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026345
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021353
Refine LS restraints NCS

Ens-ID: 1 / Number: 18175 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 143 -
Rwork0.307 2779 -
obs--97.43 %

+
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