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- PDB-4kra: Salmonella typhi OmpF complex with Ciprofloxacin -

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Basic information

Entry
Database: PDB / ID: 4kra
TitleSalmonella typhi OmpF complex with Ciprofloxacin
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN / Beta barrel / Transport / Outer membrane
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
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 / : / Porin domain superfamily / Porin ...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 / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-CPF / Outer membrane porin F
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.32 Å
AuthorsMadhuranayaki, T. / Balasubramaniam, D. / Krishnaswamy, S.
CitationJournal: To be published
Title: Salmonella typhi OmpF complex with Ciprofloxacin
Authors: Madhuranayaki, T. / Balasubramaniam, D. / Krishnaswamy, S.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,9954
Polymers113,6643
Non-polymers3311
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-50 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.160, 139.110, 151.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is as the same as asymmetric unit

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Components

#1: Protein Outer membrane protein F


Mass: 37887.957 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar typhi (bacteria)
Strain: Ty21a / Gene: ompF / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 / References: UniProt: P37432*PLUS
#2: Chemical ChemComp-CPF / 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID / ciprofloxacin


Mass: 331.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18FN3O3 / Comment: antibiotic*YM
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHCIH HAS DERIVED FROM SALMONELLA TYPHI (STRAIN ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHCIH HAS DERIVED FROM SALMONELLA TYPHI (STRAIN TY21A) DOES NOT CURRENTLY EXIST.

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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: 3.94 Å3/Da / Density % sol: 68.77 % / Mosaicity: 1.09 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Tri sodium citrate pH5.6, 0.25M potassium sodium tartrate, 2M Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.32→102.358 Å / Num. all: 27234 / Num. obs: 27234 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 83.7 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.32-3.57.10.6010.5571.32750339000.2220.6010.5573.499.6
3.5-3.717.20.3750.3482.12673137160.1380.3750.3485100
3.71-3.977.30.2440.2263.22539434910.090.2440.2267100
3.97-4.297.30.1480.13752368732660.0550.1480.13710.1100
4.29-4.77.20.1050.0976.72171330040.0390.1050.09713.5100
4.7-5.257.20.1020.0946.91974827380.0380.1020.09414.1100
5.25-6.067.10.1280.11851751724500.0470.1280.11814.7100
6.06-7.427.10.1220.1135.11474920800.0450.1220.11317100
7.42-10.56.90.0570.0539.21135716430.0220.0570.05320.8100
10.5-52.3686.30.0530.0499.859819460.0210.0530.04923.497.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.5 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.32 Å44.33 Å
Translation3.32 Å44.33 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSG

3nsg


Resolution: 3.32→50 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.844 / WRfactor Rfree: 0.3359 / WRfactor Rwork: 0.2638 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6924 / SU B: 39.362 / SU ML: 0.62 / SU Rfree: 0.6258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.626 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3388 1365 5 %RANDOM
Rwork0.2717 ---
obs0.2752 27137 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 143.78 Å2 / Biso mean: 96.5297 Å2 / Biso min: 29.72 Å2
Baniso -1Baniso -2Baniso -3
1--5.24 Å20 Å20 Å2
2--15.19 Å20 Å2
3----9.95 Å2
Refinement stepCycle: LAST / Resolution: 3.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7666 0 24 0 7690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217847
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.91310668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53351011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.78425.035423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.212151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8191535
X-RAY DIFFRACTIONr_chiral_restr0.1080.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026362
X-RAY DIFFRACTIONr_mcbond_it0.5731.54978
X-RAY DIFFRACTIONr_mcangle_it1.06427813
X-RAY DIFFRACTIONr_scbond_it0.96332869
X-RAY DIFFRACTIONr_scangle_it1.7034.52852
LS refinement shellResolution: 3.32→3.406 Å / Rfactor Rfree error: 0.626 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 107 -
Rwork0.415 1863 -
all-1970 -
obs-1970 99.29 %

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