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- PDB-8i5j: Crystal structure of chitin oligosaccharide binding protein from ... -

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Basic information

Entry
Database: PDB / ID: 8i5j
TitleCrystal structure of chitin oligosaccharide binding protein from Vibrio cholera.
ComponentsABC transporter substrate-binding protein
KeywordsSUGAR BINDING PROTEIN / chitin oligosaccharide / periplasmic / solute binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
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
ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 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

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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
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0034
Polymers121,9542
Non-polymers492
Water13,926773
1
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0012
Polymers60,9771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0012
Polymers60,9771
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.120, 81.643, 87.273
Angle α, β, γ (deg.)90.00, 104.15, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dehydrate, Polyethylene glycol 4,000

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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: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.602→19.81 Å / Num. obs: 261371 / % possible obs: 91.63 % / Redundancy: 3.27 % / CC1/2: 0.994 / Net I/σ(I): 8.75
Reflection shellResolution: 1.602→1.69 Å / Num. unique obs: 28401 / CC1/2: 0.519

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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: 4GF8

4gf8


Resolution: 1.602→19.81 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 12870 4.92 %
Rwork0.1618 --
obs0.1632 261324 91.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.602→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8475 0 2 773 9250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098717
X-RAY DIFFRACTIONf_angle_d0.96911873
X-RAY DIFFRACTIONf_dihedral_angle_d10.7745113
X-RAY DIFFRACTIONf_chiral_restr0.0641263
X-RAY DIFFRACTIONf_plane_restr0.0081547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6024-1.62060.30342000.29564441X-RAY DIFFRACTION48
1.6206-1.63960.31542730.26785285X-RAY DIFFRACTION59
1.6396-1.65960.26983010.25295629X-RAY DIFFRACTION63
1.6596-1.68060.28223190.25316129X-RAY DIFFRACTION68
1.6806-1.70270.27233220.24916725X-RAY DIFFRACTION74
1.7027-1.7260.27673740.22787369X-RAY DIFFRACTION81
1.726-1.75070.28524270.21458035X-RAY DIFFRACTION90
1.7507-1.77680.23674950.19148750X-RAY DIFFRACTION97
1.7768-1.80450.23154400.18198916X-RAY DIFFRACTION98
1.8045-1.83410.21294000.17578963X-RAY DIFFRACTION99
1.8341-1.86570.18884070.17218937X-RAY DIFFRACTION99
1.8657-1.89960.18834600.16918989X-RAY DIFFRACTION99
1.8996-1.93610.20045210.16668878X-RAY DIFFRACTION99
1.9361-1.97560.20045100.15968884X-RAY DIFFRACTION99
1.9756-2.01850.214890.15978936X-RAY DIFFRACTION99
2.0185-2.06540.19474750.16238908X-RAY DIFFRACTION99
2.0654-2.1170.20344800.15918877X-RAY DIFFRACTION99
2.117-2.17420.20784730.15088992X-RAY DIFFRACTION99
2.1742-2.23810.18194460.14838915X-RAY DIFFRACTION99
2.2381-2.31020.19734270.14868991X-RAY DIFFRACTION99
2.3102-2.39260.18414040.15469008X-RAY DIFFRACTION99
2.3926-2.48830.20164580.16718868X-RAY DIFFRACTION98
2.4883-2.60130.21954710.16478901X-RAY DIFFRACTION99
2.6013-2.73810.1954390.16548927X-RAY DIFFRACTION98
2.7381-2.90910.18064750.16198854X-RAY DIFFRACTION98
2.9091-3.13290.20585010.16338855X-RAY DIFFRACTION98
3.1329-3.44670.17914790.15278800X-RAY DIFFRACTION98
3.4467-3.94210.16144870.14418892X-RAY DIFFRACTION99
3.9421-4.95370.14534340.13458897X-RAY DIFFRACTION98
4.9537-19.810.17524830.16548903X-RAY DIFFRACTION99

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