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- PDB-2zfg: Structure of OMPF PORIN -

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Basic information

Entry
Database: PDB / ID: 2zfg
TitleStructure of OMPF PORIN
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN / OmpF PORIN / Ordered Waters / Ion transport / Membrane / Outer membrane / Phage recognition / Transmembrane / Transport
Function / homology
Function and homology information


colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity / lipid binding / membrane / identical protein binding
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 / 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: 1.59 Å
AuthorsCramer, W.A. / Zakharov, S.D. / Yamashita, E.
CitationJournal: Embo J. / Year: 2008
Title: Crystal structures of the OmpF porin: function in a colicin translocon.
Authors: Yamashita, E. / Zhalnina, M.V. / Zakharov, S.D. / Sharma, O. / Cramer, W.A.
History
DepositionJan 4, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7514
Polymers37,1141
Non-polymers6373
Water5,801322
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)113,25412
Polymers111,3433
Non-polymers1,9129
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8590 Å2
ΔGint-58 kcal/mol
Surface area40500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.923, 116.923, 51.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

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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: 37114.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompF, cmlB, coa, cry, tolF / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.94 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.59→101.02 Å / Num. obs: 53879 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
SCALEPACKdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF

2omf


Resolution: 1.59→36.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.36 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE ELECTRON DENSITY AT RESIDUE ASN27 IS SMALL; THE OCCUPANCY AT THIS SITE IN OTHER OMPF STRUCTURES, 1HXX AND 2OMF, IS ZERO. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21837 2740 5.1 %RANDOM
Rwork0.18078 ---
obs0.18256 51108 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.534 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.55 Å20 Å2
2---1.1 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.59→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 43 322 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222736
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9433689
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23325146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07415407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2581511
X-RAY DIFFRACTIONr_chiral_restr0.090.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022150
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21114
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21893
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8071.51684
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37822628
X-RAY DIFFRACTIONr_scbond_it2.16231200
X-RAY DIFFRACTIONr_scangle_it3.0924.51061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.592→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 179 -
Rwork0.227 3547 -
obs--93.64 %

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