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- PDB-1e54: Anion-selective porin from Comamonas acidovorans -

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Basic information

Entry
Database: PDB / ID: 1.0E+54
TitleAnion-selective porin from Comamonas acidovorans
Components
  • OMP32
  • OUTER MEMBRANE PORIN PROTEIN 32
KeywordsOUTER MEMBRANE PROTEIN / ANIONEN CHANNEL / CHANNEL PROTEIN / BETA BARREL
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Porin, Neisseria sp. type / Gram-negative porin / Porin domain, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin protein 32
Similarity search - Component
Biological speciesCOMAMONAS ACIDOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsZeth, K. / Diederichs, K. / Welte, W. / Engelhardt, H.
CitationJournal: Structure / Year: 2000
Title: Crystal Structure of Omp32, the Anion-Selective Porin from Comamonas Acidovorans, in Complex with a Periplasmic Peptideat 2.1 A Resolution
Authors: Zeth, K. / Diederichs, K. / Welte, W. / Engelhardt, H.
History
DepositionJul 17, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OUTER MEMBRANE PORIN PROTEIN 32
B: OMP32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8884
Polymers35,7512
Non-polymers1362
Water1,76598
1
A: OUTER MEMBRANE PORIN PROTEIN 32
B: OMP32
hetero molecules

A: OUTER MEMBRANE PORIN PROTEIN 32
B: OMP32
hetero molecules

A: OUTER MEMBRANE PORIN PROTEIN 32
B: OMP32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,66312
Polymers107,2546
Non-polymers4086
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12380 Å2
ΔGint-97.1 kcal/mol
Surface area45840 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.250, 107.250, 140.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein OUTER MEMBRANE PORIN PROTEIN 32 / OMP32


Mass: 34830.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) COMAMONAS ACIDOVORANS (bacteria) / Cellular location: OUTER MEMBRANE / References: UniProt: P24305
#2: Protein/peptide OMP32


Mass: 920.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) COMAMONAS ACIDOVORANS (bacteria) / Cellular location: OUTER MEMBRANE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: FORMS ANION SELECTIVE CHANNELS. SUBUNIT: HOMOTRIMER (BY SIMILARITY). SUBCELLULAR LOCATION: ...FUNCTION: FORMS ANION SELECTIVE CHANNELS. SUBUNIT: HOMOTRIMER (BY SIMILARITY). SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN. OUTER MEMBRANE. SIMILARITY: TO BACTERIAL OUTER MEMBRANE PROTEINS AND PORINS.

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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: 4.35 Å3/Da / Density % sol: 73 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 290 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Zeth, K., (1998) Acta Crystallogr., D54, 650.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 %beta-D-octylglucoside1reservoir
220 mMTris1reservoir
310 mg/mlprotein1drop
41.3-1.4 M1dropLi2SO4
5100 mMHEPES1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.8
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 29830 / % possible obs: 84.9 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.12
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.402 / % possible all: 72.3
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.112
Reflection shell
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.459

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1479 5 %RANDOM
Rwork0.2 ---
obs0.2 29830 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.0209 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.66 Å25.04 Å20 Å2
2--5.66 Å20 Å2
3----11.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 6 98 2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.442.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 202 5 %
Rwork0.244 3999 -
obs--72.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CA.PARSULFAT.TOP
X-RAY DIFFRACTION3SULFAT.PARCA.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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