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- PDB-7eho: Chitin oligosaccharide binding protein -

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Basic information

Entry
Database: PDB / ID: 7eho
TitleChitin oligosaccharide binding protein
ComponentsChitin oligosaccharide binding protein NagB2
KeywordsSUGAR BINDING PROTEIN / Chitin oligosaccharide binding protein
Biological speciesPaenibacillus sp. FPU-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 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 1.2May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Chitin oligosaccharide binding protein NagB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8453
Polymers94,6512
Non-polymers1941
Water16,502916
1
A: Chitin oligosaccharide binding protein NagB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5202
Polymers47,3251
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitin oligosaccharide binding protein NagB2


Theoretical massNumber of molelcules
Total (without water)47,3251
Polymers47,3251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.782, 75.978, 87.493
Angle α, β, γ (deg.)90.000, 107.130, 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FPU-7 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
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: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 65822 / % possible obs: 91.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.8 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.124 / Net I/σ(I): 20.5
Reflection shellResolution: 1.79→1.83 Å / Num. unique obs: 3323 / CC1/2: 0.701 / Rpim(I) all: 0.533 / Rrim(I) all: 1.313

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→41.81 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 3294 5.01 %
Rwork0.1781 62493 -
obs0.1795 65787 90.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.26 Å2 / Biso mean: 24.2769 Å2 / Biso min: 8.84 Å2
Refinement stepCycle: final / Resolution: 1.79→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6155 0 13 916 7084
Biso mean--30.11 31.03 -
Num. residues----808
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.79-1.820.33731360.28662376251283
1.82-1.850.32871250.26822649277493
1.85-1.880.29981390.25382609274892
1.88-1.910.2411370.24112590272791
1.91-1.940.25421550.21992615277092
1.94-1.970.26151360.20992598273491
1.97-2.010.21551330.19742608274191
2.01-2.050.24721270.19342603273091
2.05-2.10.24461410.17892563270490
2.1-2.150.21071570.18882529268690
2.15-2.20.21341480.1832579272790
2.2-2.260.23421350.17872539267490
2.26-2.330.23241320.17632571270389
2.33-2.40.20021120.17382533264588
2.4-2.490.21741260.17042529265588
2.49-2.590.2311410.17612491263287
2.59-2.710.21340.18322493262787
2.71-2.850.21951180.17782500261887
2.85-3.030.19961480.18632510265888
3.03-3.260.20571350.17152571270690
3.26-3.590.17761640.15972714287895
3.59-4.110.15671500.15072864301499
4.11-5.170.16671440.1482894303899
5.17-41.810.211210.18312965308699

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