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- PDB-3nsg: Crystal Structure of OmpF, an Outer Membrane Protein from Salmone... -

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Basic information

Entry
Database: PDB / ID: 3nsg
TitleCrystal Structure of OmpF, an Outer Membrane Protein from Salmonella typhi
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN / Porin / beta barrel / outer membrane protein / Beta Barrel Membrane protein
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. / 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
CITRATE ANION / L(+)-TARTARIC ACID / Outer membrane porin F
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å
AuthorsBalasubramaniam, D. / Arockiasamy, A. / Sharma, A. / Krishnaswamy, S.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi
Authors: Balasubramaniam, D. / Arockiasamy, A. / Kumar, P.D. / Sharma, A. / Krishnaswamy, S.
History
DepositionJul 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)131,769150
Polymers114,6493
Non-polymers17,120147
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-52 kcal/mol
Surface area41290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.185, 139.335, 150.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 38216.219 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): B834(DE3)/pLysS / References: UniProt: P37432*PLUS

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Non-polymers , 7 types, 534 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHCIH HAS DERIVED FROM SALMONELLA TYPHI DOES NOT ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHCIH HAS DERIVED FROM SALMONELLA TYPHI 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: 3.9 Å3/Da / Density % sol: 68.48 % / Mosaicity: 0.721 °
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Tri sodium citrate, 0.25M potassium sodium tartrate, 2M Ammonium sulphate, pH 5.4, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorDate: Dec 13, 2007
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 38061 / % possible obs: 84.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.092 / Χ2: 1.116 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.94.80.36425290.63157.1
2.9-3.025.40.3228860.662164.8
3.02-3.155.90.24431980.649171.8
3.15-3.326.50.20633610.661175.7
3.32-3.537.20.15137120.718182.8
3.53-3.87.70.11941070.802191.9
3.8-4.188.50.08544330.915198.6
4.18-4.799.30.07145271.181199.8
4.79-6.039.40.08445611.466199.9
6.03-5090.05547472.029199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.79→42.59 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.801 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.658 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.33672 1898 5 %RANDOM
Rwork0.25489 ---
obs0.25887 36118 84.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 150 Å2 / Biso mean: 61.787 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1--4.81 Å20 Å20 Å2
2--12.44 Å20 Å2
3----7.63 Å2
Refinement stepCycle: LAST / Resolution: 2.79→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8007 0 1038 387 9432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0219060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6562.01812181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.84851020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.11724.967459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.299151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2361542
X-RAY DIFFRACTIONr_chiral_restr0.160.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5911.55036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10527982
X-RAY DIFFRACTIONr_scbond_it1.2834024
X-RAY DIFFRACTIONr_scangle_it2.0684.54199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.794→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 93 -
Rwork0.419 1642 -
all-1735 -
obs--52.93 %

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