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- PDB-8i5k: Crystal structure of chitin oligosaccharide binding protein from ... -

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Basic information

Entry
Database: PDB / ID: 8i5k
TitleCrystal structure of chitin oligosaccharide binding protein from Vibrio cholera in complex with chitotriose.
ComponentsABC transporter substrate-binding protein
KeywordsSUGAR BINDING PROTEIN / chitin oligosaccharide / periplasmic / solute binding protein
Function / homology
Function and homology information


dipeptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
triacetyl-beta-chitotriose / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.219 Å
AuthorsOhnuma, T. / Takeshita, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation.
Authors: Ohnuma, T. / Tsujii, J. / Kataoka, C. / Yoshimoto, T. / Takeshita, D. / Lampela, O. / Juffer, A.H. / Suginta, W. / Fukamizo, T.
History
DepositionJan 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6293
Polymers60,9771
Non-polymers6522
Water10,142563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.087, 51.683, 70.328
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1067-

HOH

21A-1254-

HOH

31A-1260-

HOH

41A-1263-

HOH

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Components

#1: Protein ABC transporter substrate-binding protein / Peptide/nickel transport system substrate-binding protein


Mass: 60977.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: appA_1, appA, D6U24_16190, ERS013201_01979, ERS013202_02445, EYB64_10090, F0H40_11710, F0M16_04225, FLM12_17525
Production host: Escherichia coli (E. coli) / References: UniProt: A0A085SLP2
#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


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M Magnesium chloride hexahydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.219→19.307 Å / Num. obs: 237875 / % possible obs: 84.8 % / Redundancy: 3.45 % / CC1/2: 0.996 / Net I/σ(I): 8.82
Reflection shellResolution: 1.22→1.28 Å / Num. unique obs: 18620 / CC1/2: 0.507

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GFB

4gfb


Resolution: 1.219→19.307 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 11855 4.98 %
Rwork0.1689 --
obs0.1698 237863 84.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.219→19.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 44 563 4840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074413
X-RAY DIFFRACTIONf_angle_d0.9386015
X-RAY DIFFRACTIONf_dihedral_angle_d10.4472552
X-RAY DIFFRACTIONf_chiral_restr0.081647
X-RAY DIFFRACTIONf_plane_restr0.006779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2194-1.23330.6152680.46611684X-RAY DIFFRACTION19
1.2333-1.24780.3431570.34723596X-RAY DIFFRACTION40
1.2478-1.2630.34422000.30514001X-RAY DIFFRACTION45
1.263-1.2790.31742050.28874402X-RAY DIFFRACTION50
1.279-1.29580.27922160.27664926X-RAY DIFFRACTION55
1.2958-1.31360.26432310.26945674X-RAY DIFFRACTION63
1.3136-1.33230.28793590.26036302X-RAY DIFFRACTION72
1.3323-1.35220.26323880.25527514X-RAY DIFFRACTION84
1.3522-1.37330.27384220.25468187X-RAY DIFFRACTION92
1.3733-1.39580.23314110.22288358X-RAY DIFFRACTION94
1.3958-1.41990.24225080.21368385X-RAY DIFFRACTION95
1.4199-1.44570.23024710.20938488X-RAY DIFFRACTION96
1.4457-1.47350.22824090.1958536X-RAY DIFFRACTION96
1.4735-1.50360.20414120.1918576X-RAY DIFFRACTION96
1.5036-1.53620.22674800.18088488X-RAY DIFFRACTION96
1.5362-1.5720.20594750.18038515X-RAY DIFFRACTION96
1.572-1.61130.18515210.17418505X-RAY DIFFRACTION96
1.6113-1.65480.21474460.17718299X-RAY DIFFRACTION95
1.6548-1.70350.21644690.16988543X-RAY DIFFRACTION97
1.7035-1.75840.20544780.17048644X-RAY DIFFRACTION97
1.7584-1.82120.18564020.17098706X-RAY DIFFRACTION98
1.8212-1.89410.17884550.1738613X-RAY DIFFRACTION97
1.8941-1.98020.19864420.1658684X-RAY DIFFRACTION97
1.9802-2.08450.18064960.168519X-RAY DIFFRACTION97
2.0845-2.21490.18634580.15248556X-RAY DIFFRACTION97
2.2149-2.38560.1664260.16168471X-RAY DIFFRACTION95
2.3856-2.62520.19014350.16458708X-RAY DIFFRACTION98
2.6252-3.00380.184650.16098741X-RAY DIFFRACTION98
3.0038-3.77980.16594510.14668728X-RAY DIFFRACTION98
3.7798-19.3070.15144990.14668659X-RAY DIFFRACTION98

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