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- PDB-6zhv: Crystal structure of OmpF porin soaked in ciprofloxacin metaloant... -

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Basic information

Entry
Database: PDB / ID: 6zhv
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 / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / lipid binding / identical protein binding / membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / 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 / molecular replacement / Resolution: 1.945 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Outer membrane porin F
A: Outer membrane porin F
C: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,28125
Polymers118,0953
Non-polymers2,18522
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-186 kcal/mol
Surface area40720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.029, 112.005, 131.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 3
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.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-QLB / 2-[2-(2-octoxyethoxy)ethoxy]ethanol


Mass: 262.386 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H30O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 50% PEG 200, 0.2 M MgCl2, 0.1 M NaCacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 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: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.945→45.68 Å / Num. obs: 83824 / % possible obs: 99.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 34.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.029 / Rrim(I) all: 0.109 / Net I/σ(I): 15
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
1.95-1.9811.71.6434884441620.6860.4861.7171.391.4
10.11-45.6810.80.04375086980.9990.0140.04540.599

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.11 Å45.68 Å
Translation5.11 Å45.68 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LSF

4lsf


Resolution: 1.945→45.296 Å / FOM work R set: 0.8354 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 4172 4.98 %
Rwork0.1976 79533 -
obs0.1994 83705 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.43 Å2 / Biso mean: 29.66 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: final / Resolution: 1.945→45.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7891 0 351 173 8415
Biso mean--53.72 27.37 -
Num. residues----1022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098202
X-RAY DIFFRACTIONf_angle_d1.15611051
X-RAY DIFFRACTIONf_chiral_restr0.0851109
X-RAY DIFFRACTIONf_plane_restr0.0051477
X-RAY DIFFRACTIONf_dihedral_angle_d14.3582936
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9454-1.96750.39531220.3089224986
1.9675-1.99070.31611190.26842637100
1.9907-2.01490.28291410.24412614100
2.0149-2.04040.25971440.22812629100
2.0404-2.06730.25661540.21782615100
2.0673-2.09560.26121490.22042626100
2.0956-2.12560.23331690.22042597100
2.1256-2.15730.31751180.21692677100
2.1573-2.1910.30031470.22312611100
2.191-2.22690.2971360.21672643100
2.2269-2.26530.25781460.20722638100
2.2653-2.30650.25841510.20332632100
2.3065-2.35090.23641390.19612624100
2.3509-2.39880.28061380.19422650100
2.3988-2.4510.26631450.18692628100
2.451-2.5080.22751350.18062659100
2.508-2.57070.20551340.18242671100
2.5707-2.64020.24211420.17512632100
2.6402-2.71790.18991260.17932685100
2.7179-2.80560.19541390.17682651100
2.8056-2.90590.2111070.18092686100
2.9059-3.02220.2321310.19722704100
3.0222-3.15970.26161320.18992675100
3.1597-3.32630.2611260.19222700100
3.3263-3.53460.2251710.19132647100
3.5346-3.80740.22291360.20382694100
3.8074-4.19030.23611430.19682690100
4.1903-4.7960.18041520.17762729100
4.796-6.04020.22881400.19952750100
6.0402-45.2960.22841400.22422890100

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