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- PDB-1bt9: OMPF PORIN MUTANT D74A -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1bt9
TitleOMPF PORIN MUTANT D74A
ComponentsPROTEIN (MATRIX PORIN OUTER MEMBRANE PROTEIN F)
KeywordsMEMBRANE PROTEIN / INTEGRAL MEMBRANE PROTEIN PORIN / PORIN
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 / protein transport ...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 / protein transport / monoatomic ion channel activity / lipid binding / identical protein binding / membrane
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 / OTHER / Resolution: 3 Å
AuthorsPhilippsen, A. / Schirmer, T.
Citation
Journal: Biochemistry / Year: 1998
Title: Stability of trimeric OmpF porin: the contributions of the latching loop L2.
Authors: Phale, P.S. / Philippsen, A. / Kiefhaber, T. / Koebnik, R. / Phale, V.P. / Schirmer, T. / Rosenbusch, J.P.
#1: Journal: Nature / Year: 1992
Title: Crystal Structures Explain Functional Properties of Two E.Coli Porins
Authors: Cowan, S.W. / Schirmer, T. / Rummel, G. / Steiert, M. / Ghosh, R. / Pauptit, R.A. / Jansonius, J.N. / Rosenbusch, J.P.
History
DepositionSep 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Nov 3, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: PROTEIN (MATRIX PORIN OUTER MEMBRANE PROTEIN F)


Theoretical massNumber of molelcules
Total (without water)37,0701
Polymers37,0701
Non-polymers00
Water28816
1
A: PROTEIN (MATRIX PORIN OUTER MEMBRANE PROTEIN F)

A: PROTEIN (MATRIX PORIN OUTER MEMBRANE PROTEIN F)

A: PROTEIN (MATRIX PORIN OUTER MEMBRANE PROTEIN F)


Theoretical massNumber of molelcules
Total (without water)111,2113
Polymers111,2113
Non-polymers00
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 area8320 Å2
ΔGint-56 kcal/mol
Surface area42130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.500, 118.500, 52.700
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 PROTEIN (MATRIX PORIN OUTER MEMBRANE PROTEIN F) / MATRIX PORIN / OMPF PORIN


Mass: 37070.242 Da / Num. of mol.: 1 / Mutation: D74A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Species (production host): Escherichia coli / Production host: Escherichia coli B (bacteria) / Strain (production host): B / References: UniProt: P02931
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.88 Å3/Da / Density % sol: 57 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
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: 276 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 8162 / % possible obs: 92 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
SFALLmodel building
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SFALLphasing
RefinementMethod to determine structure: OTHER / Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -10 %RANDOM
Rwork0.191 ---
obs-8162 91 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 0 16 2640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.039
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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