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- PDB-7vu1: Chitoporin from Escherichia coli complex with chitohexaose -

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Basic information

Entry
Database: PDB / ID: 7vu1
TitleChitoporin from Escherichia coli complex with chitohexaose
ComponentsChitoporin
KeywordsMEMBRANE PROTEIN / Outer membrane protein Chitoporin specific porin
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: 1.9 Å
AuthorsSuginta, W. / Soysa, H.S.M. / Amornloetwattana, R. / van den Berg, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: To Be Published
Title: Chitporin from Escherichia coli complex with chitohexaose
Authors: Soysa, H.S.M. / Suginta, W. / 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)109,64934
Polymers99,0242
Non-polymers10,62532
Water7,981443
1
A: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,80016
Polymers49,5121
Non-polymers5,28815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,84918
Polymers49,5121
Non-polymers5,33717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.737, 58.551, 133.059
Angle α, β, γ (deg.)90.000, 110.708, 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

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Protein , 1 types, 2 molecules AB

#1: Protein Chitoporin / ChiP-III


Mass: 49512.078 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

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Sugars , 2 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 3 types, 467 molecules

#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.49 Å3/Da / Density % sol: 64.72 %
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: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97883 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 1.9→62.5 Å / Num. obs: 107599 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.85 Å2 / CC1/2: 0.974 / Net I/σ(I): 4.8
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 5303 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VTZ

7vtz


Resolution: 1.9→62.34 Å / SU ML: 0.2073 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.0807 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 5260 4.92 %
Rwork0.209 101633 -
obs0.2109 106893 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→62.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7003 0 422 443 7868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01057753
X-RAY DIFFRACTIONf_angle_d1.249610534
X-RAY DIFFRACTIONf_chiral_restr0.06751094
X-RAY DIFFRACTIONf_plane_restr0.00721321
X-RAY DIFFRACTIONf_dihedral_angle_d6.70785833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.3711680.31193322X-RAY DIFFRACTION98.7
1.92-1.940.32231900.30033332X-RAY DIFFRACTION97.91
1.94-1.970.32071770.27963317X-RAY DIFFRACTION97.95
1.97-1.990.31491860.26883340X-RAY DIFFRACTION98.66
1.99-2.020.27181880.24973330X-RAY DIFFRACTION97.02
2.02-2.050.2751700.24623278X-RAY DIFFRACTION98.23
2.05-2.080.31131810.24513330X-RAY DIFFRACTION97.88
2.08-2.110.28531600.24773346X-RAY DIFFRACTION97.55
2.11-2.140.30491560.23873384X-RAY DIFFRACTION99.13
2.14-2.170.25231530.23933373X-RAY DIFFRACTION98.41
2.17-2.210.24681620.22533355X-RAY DIFFRACTION99.21
2.21-2.250.28771700.22523398X-RAY DIFFRACTION98.67
2.25-2.30.29811920.22043347X-RAY DIFFRACTION99.55
2.3-2.340.26021650.21383426X-RAY DIFFRACTION99.45
2.34-2.390.25671440.20623404X-RAY DIFFRACTION99.72
2.39-2.450.24621880.20363379X-RAY DIFFRACTION99.72
2.45-2.510.23922170.20423376X-RAY DIFFRACTION99.5
2.51-2.580.23591560.2043376X-RAY DIFFRACTION99.02
2.58-2.650.28792070.20323430X-RAY DIFFRACTION99.84
2.65-2.740.26311740.20233377X-RAY DIFFRACTION99.8
2.74-2.840.24081840.1933402X-RAY DIFFRACTION99.75
2.84-2.950.24561770.18583451X-RAY DIFFRACTION99.86
2.95-3.090.20441660.19083422X-RAY DIFFRACTION99.92
3.09-3.250.25611830.18533417X-RAY DIFFRACTION99.86
3.25-3.450.23241550.18563458X-RAY DIFFRACTION99.97
3.45-3.720.22532140.18913393X-RAY DIFFRACTION100
3.72-4.090.22561730.18643441X-RAY DIFFRACTION99.86
4.09-4.690.18421470.17773501X-RAY DIFFRACTION99.81
4.69-5.90.1951740.18863502X-RAY DIFFRACTION99.95

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