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- PDB-7de8: Crystal Structure of outer membrane protein PorB with G103K mutat... -

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Basic information

Entry
Database: PDB / ID: 7de8
TitleCrystal Structure of outer membrane protein PorB with G103K mutations from Neisseria meningitidis W135
ComponentsOuter membrane protein
KeywordsMEMBRANE PROTEIN / porin / outer membrane protein / membrane transport
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Major outer membrane protein P.IB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsTanabe, M. / Kattner, C.
Funding support Germany, Japan, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research03Z2HN21 Germany
Japan Society for the Promotion of Science (JSPS)16K18506 Japan
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2021
Title: An antibiotic-resistance conferring mutation in a neisserial porin: Structure, ion flux, and ampicillin binding.
Authors: Bartsch, A. / Ives, C.M. / Kattner, C. / Pein, F. / Diehn, M. / Tanabe, M. / Munk, A. / Zachariae, U. / Steinem, C. / Llabres, S.
History
DepositionNov 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Outer membrane protein


Theoretical massNumber of molelcules
Total (without water)38,2511
Polymers38,2511
Non-polymers00
Water00
1
X: Outer membrane protein

X: Outer membrane protein

X: Outer membrane protein


Theoretical massNumber of molelcules
Total (without water)114,7543
Polymers114,7543
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8900 Å2
ΔGint-63 kcal/mol
Surface area44010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.396, 84.396, 107.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Outer membrane protein


Mass: 38251.434 Da / Num. of mol.: 1 / Mutation: G103K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M4GGR4

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES, pH 6.5 31% Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→43.3 Å / Num. obs: 11223 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.6
Reflection shellResolution: 2.75→2.81 Å / Rmerge(I) obs: 0.84 / Num. unique obs: 792

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VY8

3vy8


Resolution: 2.76→43.237 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.208 / SU B: 19.855 / SU ML: 0.364 / Average fsc free: 0.8231 / Average fsc work: 0.8447 / Cross valid method: FREE R-VALUE / ESU R: 2.376 / ESU R Free: 0.363
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2603 564 5.046 %
Rwork0.2132 10614 -
all0.216 --
obs-11178 99.795 %
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: 90.754 Å2
Baniso -1Baniso -2Baniso -3
1-3.893 Å21.946 Å20 Å2
2--3.893 Å20 Å2
3----12.628 Å2
Refinement stepCycle: LAST / Resolution: 2.76→43.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 0 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132664
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182397
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6383594
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5895555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.775342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71822.979141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11215436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.811514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023097
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02589
X-RAY DIFFRACTIONr_nbd_refined0.1910.2517
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.22346
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21290
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0620.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.214
X-RAY DIFFRACTIONr_nbd_other0.2540.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.25
X-RAY DIFFRACTIONr_mcbond_it6.1829.5051368
X-RAY DIFFRACTIONr_mcbond_other6.1799.5051367
X-RAY DIFFRACTIONr_mcangle_it8.91614.261710
X-RAY DIFFRACTIONr_mcangle_other8.91514.261711
X-RAY DIFFRACTIONr_scbond_it6.69610.1881296
X-RAY DIFFRACTIONr_scbond_other6.69610.1881296
X-RAY DIFFRACTIONr_scangle_it10.19114.9961884
X-RAY DIFFRACTIONr_scangle_other10.19114.9951884
X-RAY DIFFRACTIONr_lrange_it13.475110.5572947
X-RAY DIFFRACTIONr_lrange_other13.473110.5392948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.8320.313420.287792X-RAY DIFFRACTION100
2.832-2.9090.31480.309762X-RAY DIFFRACTION100
2.909-2.9930.393280.31734X-RAY DIFFRACTION100
2.993-3.0850.377360.309713X-RAY DIFFRACTION100
3.085-3.1860.531380.294706X-RAY DIFFRACTION100
3.186-3.2980.344300.261678X-RAY DIFFRACTION100
3.298-3.4220.301230.264659X-RAY DIFFRACTION99.7076
3.422-3.5610.289320.229635X-RAY DIFFRACTION99.8503
3.561-3.7190.297390.22596X-RAY DIFFRACTION100
3.719-3.90.296320.205569X-RAY DIFFRACTION100
3.9-4.1110.302310.218546X-RAY DIFFRACTION100
4.111-4.3590.253350.178514X-RAY DIFFRACTION99.8182
4.359-4.6590.179230.162495X-RAY DIFFRACTION99.2337
4.659-5.0310.221280.161447X-RAY DIFFRACTION99.1649
5.031-5.5080.221310.184403X-RAY DIFFRACTION99.5413
5.508-6.1540.245190.197376X-RAY DIFFRACTION100
6.154-7.0980.218190.211345X-RAY DIFFRACTION99.726
7.098-8.6720.241170.205283X-RAY DIFFRACTION98.6842
8.672-12.1790.30550.183230X-RAY DIFFRACTION99.5763
12.179-43.2370.12680.223130X-RAY DIFFRACTION97.8723

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