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- PDB-1hxt: OMPF PORIN MUTANT NQAAA -

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Basic information

Entry
Database: PDB / ID: 1hxt
TitleOMPF PORIN MUTANT NQAAA
ComponentsOUTER MEMBRANE PROTEIN F
KeywordsMEMBRANE PROTEIN / porin / beta barrel
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 / difference fourier / Resolution: 2.4 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)39,91811
Polymers36,8541
Non-polymers3,06410
Water99155
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)119,75533
Polymers110,5623
Non-polymers9,19330
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 area13540 Å2
ΔGint15 kcal/mol
Surface area44510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.084, 117.084, 51.344
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: 36853.934 Da / Num. of mol.: 1 / Mutation: R42A,R82A,D113N,E117Q,R132A
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.: 10 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
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: 0.992 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 53590 / Num. obs: 14853 / % possible obs: 93.1 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.31 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 53590

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: difference fourier / Resolution: 2.4→8 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 5643 based on wt selection
Rwork0.233 --
all-16124 -
obs-10481 -
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 65 55 2729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.026
X-RAY DIFFRACTIONp_bond_d0.007
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor obs: 0.213 / Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.033

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