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- PDB-7ff7: Structure of OmpF2 -

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Basic information

Entry
Database: PDB / ID: 7ff7
TitleStructure of OmpF2
ComponentsOuter membrane protein F
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
Outer membrane protein F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 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 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
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
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

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein F
B: Outer membrane protein F
C: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4826
Polymers111,2863
Non-polymers1963
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-163 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.732, 111.968, 110.873
Angle α, β, γ (deg.)90.000, 110.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer membrane protein F


Mass: 37095.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompF_1, SAMEA3751407_00438 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Z7L1X9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.01 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 mM sodium cacodylate (pH 8.0) buffer containing 45% 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: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.38→50 Å / Num. obs: 24876 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.057 / Rrim(I) all: 0.152 / Χ2: 3.935 / Net I/σ(I): 10.4 / Num. measured all: 184541
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.38-3.447.60.44112500.9730.1720.4731.999100
3.44-3.57.60.40112280.9840.1580.4311.955100
3.5-3.577.60.34612350.9840.1350.3722.101100
3.57-3.647.60.33312480.9910.1310.3582.184100
3.64-3.727.50.25712310.9930.1020.2772.271100
3.72-3.817.60.25812510.9880.1020.2782.31100
3.81-3.97.50.2412320.9850.0940.2582.376100
3.9-4.017.50.21312580.9890.0840.2292.478100
4.01-4.137.50.18512420.9910.0740.22.808100
4.13-4.267.50.15212620.9890.060.1643.047100
4.26-4.417.50.13512360.9880.0530.1453.325100
4.41-4.597.50.11912480.9920.0470.1283.694100
4.59-4.87.50.12412540.990.0490.1334.258100
4.8-5.057.50.12412370.9870.0490.1334.742100
5.05-5.367.40.11612550.9870.0460.1254.693100
5.36-5.787.40.11912470.9860.0480.1285.105100
5.78-6.367.40.11612540.9740.0470.1265.595100
6.36-7.287.30.10312630.9880.0420.1125.967100
7.28-9.167.10.10612630.9820.0440.1158.103100
9.16-506.30.11911820.9470.0570.13311.78291.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF

2omf


Resolution: 3.38→38.05 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.829 / SU B: 33.885 / SU ML: 0.549 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3371 1206 4.9 %RANDOM
Rwork0.2903 ---
obs0.2925 23204 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 207.31 Å2 / Biso mean: 88.21 Å2 / Biso min: 11.26 Å2
Baniso -1Baniso -2Baniso -3
1-5.35 Å2-0 Å21.21 Å2
2--3.92 Å2-0 Å2
3----7.9 Å2
Refinement stepCycle: final / Resolution: 3.38→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7038 0 3 14 7055
Biso mean--81.12 57.64 -
Num. residues----986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127174
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185778
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.6429765
X-RAY DIFFRACTIONr_angle_other_deg1.4571.58113224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62123.907366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97215833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8551522
X-RAY DIFFRACTIONr_chiral_restr0.0450.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021642
LS refinement shellResolution: 3.38→3.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 84 -
Rwork0.37 1699 -
all-1783 -
obs--98.51 %

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