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- PDB-7fdy: Structure of OmpF1 -

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Basic information

Entry
Database: PDB / ID: 7fdy
TitleStructure of OmpF1
ComponentsPorin OmpF
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer 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 domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJeong, W.J. / Song, W.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Not funded2019R1C1C1003863 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2022
Title: Design and directed evolution of noncanonical beta-stereoselective metalloglycosidases.
Authors: Jeong, W.J. / Song, W.J.
History
DepositionJul 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Porin OmpF
B: Porin OmpF
C: Porin OmpF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7436
Polymers111,5473
Non-polymers1963
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-175 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.600, 140.390, 110.860
Angle α, β, γ (deg.)90.000, 120.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Porin OmpF


Mass: 37182.324 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompF, D2185_10280 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A418U3R0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 mM sodium cacodylate (pH 8.0), 43% PEG 200, 0.12 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.1→29.128 Å / Num. obs: 60349 / % possible obs: 98.3 % / Redundancy: 3.747 % / Biso Wilson estimate: 71.244 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.127 / Χ2: 0.84 / Net I/σ(I): 10.33 / Num. measured all: 226132
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.283.720.7771.5536007986696780.8390.90898.1
3.28-3.513.8080.4083.0134936924891740.9440.47699.2
3.51-3.783.7990.2514.5532082858284450.9870.29398.4
3.78-4.143.7960.1667.0329449795577580.9880.19497.5
4.14-4.613.7640.08612.8726321712769920.9950.10198.1
4.61-5.33.7710.06615.9123777637263050.9970.07798.9
5.3-6.443.7440.05718.7720038539153520.9970.06799.3
6.44-8.93.660.04126.3315372423142000.9980.04899.3
8.9-29.1283.3330.02935.318150261624450.9980.03493.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF

2omf


Resolution: 3.1→29.128 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2948 1532 5 %
Rwork0.2693 29111 -
obs0.2706 30643 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.89 Å2 / Biso mean: 86.5302 Å2 / Biso min: 37.21 Å2
Refinement stepCycle: final / Resolution: 3.1→29.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7569 0 3 3 7575
Biso mean--82.2 58.67 -
Num. residues----1014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.20010.44111390.3787263599
3.2001-3.31430.39231400.3225264099
3.3143-3.44680.37581390.2961263799
3.4468-3.60340.31111370.2919263399
3.6034-3.7930.34451390.2927262999
3.793-4.030.36851380.2875261498
4.03-4.34030.29181380.2689262899
4.3403-4.77530.24451400.2311266099
4.7753-5.46240.23571390.23392656100
5.4624-6.86710.23531410.24272683100
6.8671-29.1280.28851420.2724269699

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