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- PDB-6ehf: OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae... -

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Basic information

Entry
Database: PDB / ID: 6ehf
TitleOmpT (in-vitro folded), an outer membrane protein Vibrio cholerae (trimer form)
ComponentsOmpT protein
KeywordsMEMBRANE PROTEIN / Outer membrane protein / Porin / OmpF or OmpC ortholog / ion-transport / membrane beta barrel / ion-channel / diffusion porin / diffusion channel / non-specific porin.
Function / homology
Function and homology information


porin activity / cell outer membrane / metal ion binding
Similarity search - Function
Gram-negative porin / Porin domain, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
Authorsvan den berg, B. / Pathania, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiatives Joint Undertaking115525 United Kingdom
CitationJournal: Structure / Year: 2018
Title: Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae.
Authors: Pathania, M. / Acosta-Gutierrez, S. / Bhamidimarri, S.P. / Basle, A. / Winterhalter, M. / Ceccarelli, M. / van den Berg, B.
History
DepositionSep 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OmpT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8222
Polymers34,7821
Non-polymers401
Water19811
1
A: OmpT protein
hetero molecules

A: OmpT protein
hetero molecules

A: OmpT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4666
Polymers104,3453
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area5950 Å2
ΔGint-75 kcal/mol
Surface area43850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.910, 200.910, 200.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein OmpT protein


Mass: 34781.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: KEGG entry VC0395_A1445
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Gene: ompT, VC0395_A1445 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AME7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.45 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.05 M calcium chloride dihydrate, 0.05 M barium chloride, 0.1 M tris, 32% PEG 400

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.72→71.03 Å / Num. obs: 18714 / % possible obs: 99 % / Redundancy: 42.2 % / CC1/2: 1 / Rpim(I) all: 0.025 / Net I/σ(I): 22.1
Reflection shellHighest resolution: 2.72 Å / Redundancy: 43.7 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.6 / Rpim(I) all: 0.679 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHD

6ehd


Resolution: 2.72→71.03 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.094 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28059 956 5.1 %RANDOM
Rwork0.23798 ---
obs0.24015 17747 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.065 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.72→71.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 1 12 2464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022505
X-RAY DIFFRACTIONr_bond_other_d0.0020.022166
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9353399
X-RAY DIFFRACTIONr_angle_other_deg1.03635014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0455316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92424.96125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.628157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.6299.6061270
X-RAY DIFFRACTIONr_mcbond_other7.6299.6071269
X-RAY DIFFRACTIONr_mcangle_it10.55214.41584
X-RAY DIFFRACTIONr_mcangle_other10.54914.3991585
X-RAY DIFFRACTIONr_scbond_it8.33310.0671233
X-RAY DIFFRACTIONr_scbond_other8.33310.0681233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.6714.9291815
X-RAY DIFFRACTIONr_long_range_B_refined13.9032626
X-RAY DIFFRACTIONr_long_range_B_other13.9012626
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 80 -
Rwork0.386 1294 -
obs--100 %

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