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- PDB-3hw9: Cation selective pathway of OmpF porin revealed by anomalous x-ra... -

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Basic information

Entry
Database: PDB / ID: 3hw9
TitleCation selective pathway of OmpF porin revealed by anomalous x-ray diffraction
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN / ion transport / porin / integral membrane protein porin / Cell membrane / Cell outer membrane / Membrane / Phage recognition / Transmembrane / Transport
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / 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. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...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
: / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsBalasundaresan, D. / Raychaudhury, S. / Blachowicz, L. / Roux, B.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction.
Authors: Dhakshnamoorthy, B. / Raychaudhury, S. / Blachowicz, L. / Roux, B.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,52210
Polymers78,7302
Non-polymers7928
Water2,414134
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)119,16612
Polymers118,0953
Non-polymers1,0719
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 area11800 Å2
ΔGint-90 kcal/mol
Surface area41100 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)119,40018
Polymers118,0953
Non-polymers1,30515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area13160 Å2
ΔGint-69 kcal/mol
Surface area40500 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-29 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.545, 117.545, 121.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 39365.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0929, cmlB, coa, cry, JW0912, ompF, tolF / Plasmid: pPR272 / Production host: Escherichia coli (E. coli) / Strain (production host): MH225 / References: UniProt: P02931
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.5M NaCl, Na Phosphate pH 6.5, 0.9% BOG, 0.09% octylPOE and 14-18% PEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2007
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 26020 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 28.9
Reflection shellResolution: 2.61→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.51 / Num. unique all: 2154 / % possible all: 74.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OMF

2omf


Resolution: 2.61→46.93 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.847 / SU B: 12.978 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.877 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30028 1323 5.1 %RANDOM
Rwork0.22876 ---
obs0.23246 24470 89.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.921 Å2
Baniso -1Baniso -2Baniso -3
1--5.72 Å2-2.86 Å20 Å2
2---5.72 Å20 Å2
3---8.58 Å2
Refinement stepCycle: LAST / Resolution: 2.61→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 44 134 5416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0225384
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7951.9367266
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7545674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34324.966290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.01615798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0131522
X-RAY DIFFRACTIONr_chiral_restr0.1770.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024292
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.22493
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.23607
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2440.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4431.53300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5525206
X-RAY DIFFRACTIONr_scbond_it4.19832084
X-RAY DIFFRACTIONr_scangle_it6.3944.52060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 69 -
Rwork0.254 1473 -
obs--73.15 %

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