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- PDB-7eqr: Crystal structure of Truncated (Delta 1-19) Chitoporin VhChiP fro... -

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Basic information

Entry
Database: PDB / ID: 7eqr
TitleCrystal structure of Truncated (Delta 1-19) Chitoporin VhChiP from Vibrio harveyi in complex with chitohexaose
ComponentsChitoporin
KeywordsMEMBRANE PROTEIN / Outer-membrane protein / Sugar-specific porin / Marine bacteria / Chitooligosacharide / Porin
Function / homologyGram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin domain superfamily / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / Chitoporin
Function and homology information
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75003171354 Å
AuthorsAunkham, A. / Sanram, S. / Suginta, S.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To Be Published
Title: Structure of truncated VhChiP complex with chitohexaose
Authors: Aunkham, A. / Sanram, S. / Suginta, S.
History
DepositionMay 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: Chitoporin
B: Chitoporin
C: Chitoporin
D: Chitoporin
E: Chitoporin
F: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,99153
Polymers218,8176
Non-polymers13,17447
Water5,477304
1
A: Chitoporin
B: Chitoporin
C: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,61930
Polymers109,4093
Non-polymers7,21127
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Chitoporin
E: Chitoporin
F: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,37223
Polymers109,4093
Non-polymers5,96420
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.000, 131.226, 136.586
Angle α, β, γ (deg.)65.799, 87.826, 86.897
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Chitoporin


Mass: 36469.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP / Production host: Escherichia coli (E. coli) / References: UniProt: L0RVU0

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Sugars , 5 types, 7 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 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]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#4: 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


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#5: 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 natural 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 344 molecules

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


Mass: 306.438 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#8: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.8
Details: 10 mM GlcNAc6 , 0.125 M Lithium nitrate, 0.1 M Glycine pH 9.8, 45 % v/v PEG 400

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2020
Details: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors
RadiationMonochromator: LN2-Cooled Fixed Exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 98809 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.75 / CC star: 0.926 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.081 / Rrim(I) all: 0.188 / Rsym value: 0.138 / Χ2: 0.95 / Net I/σ(I): 37.7
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 98809 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.03

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDO

5mdo


Resolution: 2.75003171354→19.8910427457 Å / SU ML: 0.295385871173 / Cross valid method: NONE / σ(F): 1.96346217736 / Phase error: 23.4658288747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222748080602 4784 5.56946109876 %
Rwork0.179783098027 81113 -
obs0.182204428945 85897 90.3627259147 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.2929439915 Å2
Refinement stepCycle: LAST / Resolution: 2.75003171354→19.8910427457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15462 0 684 304 16450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0090821632159316524
X-RAY DIFFRACTIONf_angle_d1.0417057067222333
X-RAY DIFFRACTIONf_chiral_restr0.05393997289532216
X-RAY DIFFRACTIONf_plane_restr0.0050913979522939
X-RAY DIFFRACTIONf_dihedral_angle_d15.2919465259336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75003171354-2.78120.282641285062830.2238247579151818X-RAY DIFFRACTION60.4259376987
2.7812-2.81380.2680134985141130.2154432566151920X-RAY DIFFRACTION64.4169835234
2.8138-2.8480.289880945607980.2011063566612015X-RAY DIFFRACTION66.8247944339
2.848-2.8840.2792529581431250.2137994611092102X-RAY DIFFRACTION69.59375
2.884-2.92180.2419991636741190.2139498291872242X-RAY DIFFRACTION74.904822335
2.9218-2.96170.2532697586681250.2116309089812335X-RAY DIFFRACTION78.3439490446
2.9617-3.00390.267250732191390.2166039612182388X-RAY DIFFRACTION79.6407185629
3.0039-3.04860.2649944940661650.2316180181682548X-RAY DIFFRACTION83.2719459791
3.0486-3.0960.2733643354771450.2171048971742509X-RAY DIFFRACTION85.5025773196
3.096-3.14660.2869740958851850.2080386287822545X-RAY DIFFRACTION87.5280538634
3.1466-3.20070.2426516423541880.2049987554692712X-RAY DIFFRACTION89.8110870238
3.2007-3.25860.2514850032821880.1957941310792781X-RAY DIFFRACTION93.0137844612
3.2586-3.3210.2600223552861720.1948063717082823X-RAY DIFFRACTION95.4125517681
3.321-3.38850.2329376031631680.1931322704372919X-RAY DIFFRACTION97.1977329975
3.3885-3.46180.2394406042581510.1870998884852954X-RAY DIFFRACTION97.9495268139
3.4618-3.54190.2270877525681630.1836695862432931X-RAY DIFFRACTION98.5350318471
3.5419-3.62990.2103201393931820.1871293136452989X-RAY DIFFRACTION98.8774555659
3.6299-3.72740.2177662567551570.1778157798192940X-RAY DIFFRACTION99.072296865
3.7274-3.83640.238813071151740.175601922483011X-RAY DIFFRACTION99.0976975731
3.8364-3.95930.241260764851870.1870066593952924X-RAY DIFFRACTION99.076433121
3.9593-4.09960.2129874546591620.1880012348552999X-RAY DIFFRACTION99.1841857546
4.0996-4.26220.2264108606971760.1772934038482953X-RAY DIFFRACTION99.1130820399
4.2622-4.45410.2133829727611900.158794319922973X-RAY DIFFRACTION99.1846973973
4.4541-4.6860.1830687977231950.1482809313422925X-RAY DIFFRACTION99.1105463787
4.686-4.97530.1839223708641230.1363683680642989X-RAY DIFFRACTION99.2663476874
4.9753-5.35250.1839968821831530.151929784053028X-RAY DIFFRACTION99.4373241638
5.3525-5.87850.1922868199462110.1689089597432960X-RAY DIFFRACTION99.4043887147
5.8785-6.70050.2172432871852250.1710206620572900X-RAY DIFFRACTION99.5539980886
6.7005-8.33720.1900622081461970.1700098734422993X-RAY DIFFRACTION99.6563573883
8.3372-19.89104274570.1970338177651250.1819086568962987X-RAY DIFFRACTION98.6370839937

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