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- PDB-7q5c: Crystal structure of OmpG in space group 96 -

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Basic information

Entry
Database: PDB / ID: 7q5c
TitleCrystal structure of OmpG in space group 96
ComponentsOuter membrane porin G
KeywordsMEMBRANE PROTEIN / OmpG / Channel / Membrane / Oligosaccharide
Function / homology
Function and homology information


carbohydrate transmembrane transport / oligosaccharide transporting porin activity / maltose transporting porin activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane porin G / Outer membrane protein G (OmpG)
Similarity search - Domain/homology
Outer membrane porin G
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.717 Å
AuthorsNguyen, T.T.M. / Khan, A.R. / Barringer, R. / McManus, J.J. / Race, P.R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission722687European Union
CitationJournal: To Be Published
Title: Experimental phase diagrams to optimise OmpG
Authors: Nguyen, T.T.M. / Khan, A.R. / Barringer, R. / McManus, J.J. / Race, P.R.
History
DepositionNov 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
XXX: Outer membrane porin G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9336
Polymers32,9371
Non-polymers9965
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint2 kcal/mol
Surface area14870 Å2
Unit cell
Length a, b, c (Å)71.343, 71.343, 200.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11XXX-515-

HOH

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Components

#1: Protein Outer membrane porin G / Outer membrane protein G / OmpG


Mass: 32936.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues showing unresolvable side chains (i.e. with low confidence regarding fit to electron density) have been represented as Alanines in lieu of the bona fide residues.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ompG, b1319, JW1312 / Production host: Escherichia coli (E. coli) / References: UniProt: P76045
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.41 Å3/Da / Density % sol: 72.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.6
Details: 30-60 mM Sodium Citrate, 50-70mM NaCl, 12-14 % (w/v) PEG-3350, 60-65 mM n-octyl-beta-d-glucoside, 6-12 mg/mL protein
Temp details: 20/21 celsius

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.717→67.304 Å / Num. obs: 14670 / % possible obs: 99.7 % / Redundancy: 2 % / Rrim(I) all: 0.0247 / Net I/σ(I): 16.9
Reflection shellResolution: 2.717→2.788 Å / Num. unique obs: 980 / Rrim(I) all: 0.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Cootmodel building
xia2data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2iwv

2iwv


Resolution: 2.717→67.304 Å / Cor.coef. Fo:Fc: 0.829 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: FREE R-VALUE / ESU R: 0.518 / ESU R Free: 0.37
Details: Hydrogens have been used in their riding positions for refinement.
RfactorNum. reflection% reflection
Rfree0.328 1453 9.905 %
Rwork0.274 13217 -
all0.278 --
obs-14670 99.633 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 77.184 Å2
Baniso -1Baniso -2Baniso -3
1--3.734 Å2-0 Å2-0 Å2
2---3.734 Å20 Å2
3---7.469 Å2
Refinement stepCycle: LAST / Resolution: 2.717→67.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 61 17 2134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132178
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171831
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.6642953
X-RAY DIFFRACTIONr_angle_other_deg2.5031.6134234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8625250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7422.647136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05615285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0721512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022473
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02531
X-RAY DIFFRACTIONr_nbd_refined0.1970.2354
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.21677
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2918
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0950.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.25
X-RAY DIFFRACTIONr_nbd_other0.1640.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.22
X-RAY DIFFRACTIONr_mcbond_it7.5038.2061012
X-RAY DIFFRACTIONr_mcbond_other7.4998.2061011
X-RAY DIFFRACTIONr_mcangle_it10.61412.2871258
X-RAY DIFFRACTIONr_mcangle_other10.61212.2861259
X-RAY DIFFRACTIONr_scbond_it8.1598.6631166
X-RAY DIFFRACTIONr_scbond_other8.1568.6641166
X-RAY DIFFRACTIONr_scangle_it11.43512.8591695
X-RAY DIFFRACTIONr_scangle_other11.43312.8591696
X-RAY DIFFRACTIONr_lrange_it14.1188.6422248
X-RAY DIFFRACTIONr_lrange_other14.10788.6552245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.717-2.7880.368890.397925X-RAY DIFFRACTION95.7507
2.788-2.8640.356980.358931X-RAY DIFFRACTION99.806
2.864-2.9470.402970.322904X-RAY DIFFRACTION100
2.947-3.0380.434900.31882X-RAY DIFFRACTION100
3.038-3.1370.345970.283864X-RAY DIFFRACTION100
3.137-3.2480.3141090.261821X-RAY DIFFRACTION100
3.248-3.370.299770.236814X-RAY DIFFRACTION100
3.37-3.5080.2941000.216742X-RAY DIFFRACTION100
3.508-3.6640.3820.235744X-RAY DIFFRACTION99.8791
3.664-3.8420.372690.238729X-RAY DIFFRACTION100
3.842-4.050.347780.257682X-RAY DIFFRACTION100
4.05-4.2960.279570.24660X-RAY DIFFRACTION100
4.296-4.5920.27810.202613X-RAY DIFFRACTION100
4.592-4.960.286610.218565X-RAY DIFFRACTION100
4.96-5.4330.304610.236537X-RAY DIFFRACTION100
5.433-6.0740.344550.277490X-RAY DIFFRACTION100
6.074-7.0120.352490.219438X-RAY DIFFRACTION99.7951
7.012-8.5860.313400.256383X-RAY DIFFRACTION100
8.586-12.1310.414340.282307X-RAY DIFFRACTION99.7076
12.131-67.3040.366290.548186X-RAY DIFFRACTION100

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