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- PDB-3uu2: Salmonella typhi osmoporin(OmpC):an Outer Membrane Protein -

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Basic information

Entry
Database: PDB / ID: 3uu2
TitleSalmonella typhi osmoporin(OmpC):an Outer Membrane Protein
ComponentsOuter membrane protein C
KeywordsMEMBRANE PROTEIN / Beta Barrel / Non specific porin / osmoporin / 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, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin C / Outer membrane porin C
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsPrasanth, P. / Putcha, B.K. / Arockiasamy, A. / Krishnaswamy, S.
CitationJournal: To be Published
Title: Crystal Structure of Outer membrane protein OmpC from Salmonella typhi.
Authors: Prasanth, P. / Putcha, B.K. / Arockiasamy, A. / Krishnaswamy, S.
History
DepositionNov 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein C
B: Outer membrane protein C
C: Outer membrane protein C


Theoretical massNumber of molelcules
Total (without water)117,6213
Polymers117,6213
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-57 kcal/mol
Surface area39660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.201, 108.568, 113.391
Angle α, β, γ (deg.)90.00, 117.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer membrane protein C / Porin ompC


Mass: 39207.059 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: Ty21a / Gene: ompC, STM2267 / Plasmid: pET21b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A263, UniProt: P0A264*PLUS

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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: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 298.15 K / Method: microbatch under oil / pH: 8.5
Details: 0.01M Nickel(II) chloride hexahydrate, 0.1M Tris, 20% PEG MME 2000, pH 8.5, Microbatch under oil, temperature 298.15K

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Data collection

DiffractionMean temperature: 77.03 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0048 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0048 Å / Relative weight: 1
ReflectionResolution: 3.33→100.27 Å / Num. all: 28544 / Num. obs: 27261 / % possible obs: 95.7 % / Redundancy: 12.1 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 23
Reflection shellResolution: 3.59→3.67 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.95 / % possible all: 93.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPG

3upg


Resolution: 3.59→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.848 / SU B: 130.247 / SU ML: 0.857 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.35808 1170 5.1 %RANDOM
Rwork0.30196 ---
obs0.3049 21573 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 225.198 Å2
Baniso -1Baniso -2Baniso -3
1-4.96 Å20 Å2-1.66 Å2
2--7.52 Å20 Å2
3----14.02 Å2
Refinement stepCycle: LAST / Resolution: 3.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6988 0 0 0 6988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227144
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9269663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4215882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13725.076396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.251151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8051521
X-RAY DIFFRACTIONr_chiral_restr0.1050.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025739
X-RAY DIFFRACTIONr_mcbond_it0.5711.54341
X-RAY DIFFRACTIONr_mcangle_it1.10426843
X-RAY DIFFRACTIONr_scbond_it1.1532803
X-RAY DIFFRACTIONr_scangle_it1.9974.52820
LS refinement shellResolution: 3.59→3.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 80 -
Rwork0.376 1492 -
obs--93.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5299-1.5963-3.75594.6944-0.215213.0688-1.33391.2656-1.8558-0.7128-0.1781-0.04671.8538-0.71251.51210.6887-0.3760.38390.5287-0.44590.7645-20.1194-42.878425.1783
25.72010.2118-3.68924.4353-1.30378.43280.9894-0.2960.6286-0.2053-0.2135-0.738-3.46992.7482-0.77591.7876-1.35270.29811.3591-0.33250.5842-1.3387-9.6130.0583
34.82571.0771-1.60633.6957-0.48016.55540.71931.82820.5995-0.8199-0.12060.6219-3.3187-2.4214-0.59872.10881.24230.05421.98050.42070.4828-38.0577-9.277420.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 357
2X-RAY DIFFRACTION2B1 - 357
3X-RAY DIFFRACTION3C1 - 357

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