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- PDB-7ehu: Chitin oligosaccharide binding protein -

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Basic information

Entry
Database: PDB / ID: 7ehu
TitleChitin oligosaccharide binding protein
ComponentsChitin oligosaccharide binding protein NagB2
KeywordsSUGAR BINDING PROTEIN / Chitin oligosaccharide binding protein
Function / homologytriacetyl-beta-chitotriose / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPaenibacillus sp. FPU-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsItoh, T. / Hibi, T. / Kimoto, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K08114 Japan
Japan Society for the Promotion of Science (JSPS)19K06340 Japan
CitationJournal: J Struct Biol X / Year: 2021
Title: Structural characterization of two solute-binding proteins for N,N' -diacetylchitobiose/ N,N',N'' -triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7.
Authors: Itoh, T. / Yaguchi, M. / Nakaichi, A. / Yoda, M. / Hibi, T. / Kimoto, H.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin oligosaccharide binding protein NagB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0593
Polymers47,3251
Non-polymers7342
Water11,512639
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint15 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.241, 69.616, 56.195
Angle α, β, γ (deg.)90.000, 108.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chitin oligosaccharide binding protein NagB2


Mass: 47325.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FPU-7 (bacteria) / Production host: Escherichia coli (E. coli)
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG3350, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.85 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 114172 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 10.9 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 41.6
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 5714 / CC1/2: 0.702 / Rpim(I) all: 0.474 / Rrim(I) all: 1.279

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EHO

7eho


Resolution: 1.2→29.15 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1636 5779 5.06 %
Rwork0.1405 108345 -
obs0.1417 114124 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.64 Å2 / Biso mean: 18.9952 Å2 / Biso min: 7.19 Å2
Refinement stepCycle: final / Resolution: 1.2→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 99 639 3818
Biso mean--16.8 29.18 -
Num. residues----405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.210.23931680.22813416358496
1.21-1.230.24461650.220836883853100
1.23-1.240.22281810.216736093790100
1.24-1.260.23692050.203435923797100
1.26-1.280.23551960.195435863782100
1.28-1.290.21661900.197635873777100
1.29-1.310.2191790.188636533832100
1.31-1.330.22612070.181635833790100
1.33-1.350.22911990.176235873786100
1.35-1.370.18562020.167536023804100
1.37-1.40.19881760.157536423818100
1.4-1.420.16822140.149535633777100
1.42-1.450.16721710.146136333804100
1.45-1.480.20012010.141736473848100
1.48-1.510.15342230.142735383761100
1.51-1.550.16881770.131836143791100
1.55-1.590.15852020.127136253827100
1.59-1.630.16691910.120336173808100
1.63-1.680.13631940.122636063800100
1.68-1.730.17831810.130736393820100
1.73-1.790.16892020.137136063808100
1.79-1.860.15212070.135436083815100
1.87-1.950.16881730.140436473820100
1.95-2.050.16082050.133135723777100
2.05-2.180.14282000.125636523852100
2.18-2.350.15721980.125236053803100
2.35-2.590.13221900.129336403830100
2.59-2.960.15141900.131536523842100
2.96-3.730.15732030.131236413844100
3.73-29.150.14841890.13813695388499

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