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- PDB-1hxx: OMPF PORIN MUTANT Y106F -

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Basic information

Entry
Database: PDB / ID: 1hxx
TitleOMPF PORIN MUTANT Y106F
ComponentsOUTER MEMBRANE PROTEIN F
KeywordsMEMBRANE PROTEIN / porin / beta barrel
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / 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. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / 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 / difference fourier / Resolution: 2.2 Å
AuthorsPhale, P.S. / Philippsen, A. / Widmer, C. / Phale, V.P. / Rosenbusch, J.P. / Schirmer, T.
CitationJournal: Biochemistry / Year: 2001
Title: Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation.
Authors: Phale, P.S. / Philippsen, A. / Widmer, C. / Phale, V.P. / Rosenbusch, J.P. / Schirmer, T.
History
DepositionJan 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Oct 27, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)38,3245
Polymers37,0981
Non-polymers1,2264
Water2,612145
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)114,97215
Polymers111,2953
Non-polymers3,67712
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 area11810 Å2
ΔGint4 kcal/mol
Surface area41020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.105, 118.105, 52.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein OUTER MEMBRANE PROTEIN F / PORIN OMPF


Mass: 37098.250 Da / Num. of mol.: 1 / Mutation: Y106F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


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


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal grow
*PLUS
Method: microdialysis / Details: Pauptit, R.A., (1991) J. Mol. Biol., 218, 505.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
210.5 %PEG200012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.042 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.042 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 71614 / Num. obs: 19807 / % possible obs: 79.9 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7
Reflection
*PLUS
% possible obs: 97.9 % / Num. measured all: 71614

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: difference fourier / Resolution: 2.2→8 Å / Stereochemistry target values: engh & huber
RfactorNum. reflectionSelection details
Rfree0.249 2984 based on wt selection
Rwork0.187 --
all-29859 -
obs-26873 -
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 21 145 2792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.08
X-RAY DIFFRACTIONp_angle_d0.028
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174 / Rfactor Rfree: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.08

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