[English] 日本語
Yorodumi
- PDB-6zhp: Crystal structure of OmpF porin soaked in ciprofloxacin metaloant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zhp
TitleCrystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
ComponentsOuter membrane porin F
KeywordsMEMBRANE PROTEIN / OmpF / porin
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 domain superfamily
Similarity search - Domain/homology
2-[2-(2-octoxyethoxy)ethoxy]ethanol / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å
AuthorsSousa, C.F. / Morais-Cabral, J. / Gameiro, P.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) Portugal
CitationJournal: To Be Published
Title: Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
Authors: Sousa, C.F. / Morais-Cabral, J. / Gameiro, P.
History
DepositionJun 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9375
Polymers39,3651
Non-polymers5724
Water2,774154
1
B: Outer membrane porin F
hetero molecules

B: Outer membrane porin F
hetero molecules

B: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,81115
Polymers118,0953
Non-polymers1,71612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area9370 Å2
ΔGint-109 kcal/mol
Surface area40720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.943, 135.943, 51.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

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


Mass: 39365.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Plasmid: PRSF-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02931
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-QLB / 2-[2-(2-octoxyethoxy)ethoxy]ethanol


Mass: 262.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 22 % PEG 2000, 0.25 M MgCl2, 0.1 M Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980131 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980131 Å / Relative weight: 1
ReflectionResolution: 2.05→47.46 Å / Num. obs: 34532 / % possible obs: 99.6 % / Redundancy: 19.9 % / Biso Wilson estimate: 34.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.042 / Rrim(I) all: 0.186 / Net I/σ(I): 13 / Num. measured all: 688820 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.1118.61.5324738725460.5550.3591.5751.994.8
8.95-47.4618.20.05582994570.9990.0130.05736.599

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LSF

4lsf


Resolution: 2.053→47.46 Å / FOM work R set: 0.8672 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1679 4.86 %
Rwork0.1786 32845 -
obs0.18 34524 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.82 Å2 / Biso mean: 36.93 Å2 / Biso min: 21.18 Å2
Refinement stepCycle: final / Resolution: 2.053→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 98 154 2884
Biso mean--58.8 39.73 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072736
X-RAY DIFFRACTIONf_angle_d1.1083692
X-RAY DIFFRACTIONf_chiral_restr0.078372
X-RAY DIFFRACTIONf_plane_restr0.004495
X-RAY DIFFRACTIONf_dihedral_angle_d14.036976
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0533-2.11370.27711120.2311263496
2.1137-2.18190.26031380.21672718100
2.1819-2.25990.24611330.2162732100
2.2599-2.35040.25531270.19522759100
2.3504-2.45740.29341480.21652690100
2.4574-2.58690.25131400.18822739100
2.5869-2.7490.20081510.16692718100
2.749-2.96120.19271410.17332729100
2.9612-3.25910.17761470.16872746100
3.2591-3.73060.20831540.16542750100
3.7306-4.69950.17791290.16382787100
4.6995-47.460.19281590.18092843100

+
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