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- PDB-7vu0: Chitoporin from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 7vu0
TitleChitoporin from Escherichia coli
ComponentsChitoporin
KeywordsMEMBRANE PROTEIN / Outer membrane protein Chitoporin specific channel
Function / homology
Function and homology information


diacetylchitobiose metabolic process / oligosaccharide transport / polysaccharide transport / porin activity / pore complex / monoatomic ion transport / cell outer membrane / channel activity
Similarity search - Function
Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSuginta, W. / Soysa, H.S.M. / Amornloetwattana, R. / van den Berg, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Chitoporin from Escherichia coli
Authors: Suginta, W. / Soysa, H.S.M. / Amornloetwattana, R. / van den Berg, B.
History
DepositionNov 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitoporin
B: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,82263
Polymers100,6822
Non-polymers17,14061
Water10,052558
1
A: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,42729
Polymers50,3411
Non-polymers8,08628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,39534
Polymers50,3411
Non-polymers9,05433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.077, 58.864, 134.709
Angle α, β, γ (deg.)90.000, 110.826, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Chitoporin / ChiP-III


Mass: 50340.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: chiP, ybfM, b0681, JW0667 / Production host: Escherichia coli (E. coli) / References: UniProt: P75733
#2: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM
#3: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.54 Å3/Da / Density % sol: 65.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30-35 % PEG 400, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.85→63.25 Å / Num. obs: 124529 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.29 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.4
Reflection shellResolution: 1.85→1.85 Å / Num. unique obs: 6172 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VTZ

7vtz


Resolution: 1.85→63.25 Å / SU ML: 0.2165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 5913 4.93 %
Rwork0.2154 113952 -
obs0.2172 119865 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.92 Å2
Refinement stepCycle: LAST / Resolution: 1.85→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7002 0 571 558 8131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01337856
X-RAY DIFFRACTIONf_angle_d1.148710516
X-RAY DIFFRACTIONf_chiral_restr0.07841027
X-RAY DIFFRACTIONf_plane_restr0.00851309
X-RAY DIFFRACTIONf_dihedral_angle_d16.46241320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.32561920.32793756X-RAY DIFFRACTION99.55
1.87-1.890.37061920.31823753X-RAY DIFFRACTION99.45
1.89-1.920.36292200.31043795X-RAY DIFFRACTION99.58
1.92-1.940.34792020.30853737X-RAY DIFFRACTION99.29
1.94-1.970.34152060.31083775X-RAY DIFFRACTION99.33
1.97-1.990.31621750.28973748X-RAY DIFFRACTION99.29
1.99-2.020.30282040.27293781X-RAY DIFFRACTION99.18
2.02-2.050.30031840.25683798X-RAY DIFFRACTION99.35
2.05-2.080.29051710.25273781X-RAY DIFFRACTION98.87
2.08-2.120.27121790.25123790X-RAY DIFFRACTION99.35
2.12-2.150.29382040.24933748X-RAY DIFFRACTION99.35
2.15-2.190.28111840.24323785X-RAY DIFFRACTION99.3
2.19-2.240.28362030.23863768X-RAY DIFFRACTION99.45
2.24-2.280.30252040.2333785X-RAY DIFFRACTION99.35
2.28-2.330.28812060.22643793X-RAY DIFFRACTION99.65
2.33-2.390.26481910.22173774X-RAY DIFFRACTION99.8
2.39-2.440.26051800.22133872X-RAY DIFFRACTION99.8
2.44-2.510.23562380.20633714X-RAY DIFFRACTION99.92
2.51-2.580.26831870.20573840X-RAY DIFFRACTION99.65
2.58-2.670.2552260.20393786X-RAY DIFFRACTION99.73
2.67-2.760.26741970.20273783X-RAY DIFFRACTION99.85
2.76-2.870.22442060.18923809X-RAY DIFFRACTION99.8
2.87-30.22091950.19023836X-RAY DIFFRACTION99.83
3-3.160.21211870.19523804X-RAY DIFFRACTION99.95
3.16-3.360.24571960.18273837X-RAY DIFFRACTION99.95
3.36-3.620.23322120.18513850X-RAY DIFFRACTION99.88
3.62-3.990.22442140.19233844X-RAY DIFFRACTION99.93
3.99-4.560.20751730.18543885X-RAY DIFFRACTION99.95
4.56-5.750.21311830.18663902X-RAY DIFFRACTION99.88
5.75-63.250.23852020.22223823X-RAY DIFFRACTION95.54

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