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

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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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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.: 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


Mass: 18.015 Da / Num. of mol.: 154 / 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: 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

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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

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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

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