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- PDB-7ehp: Chitin oligosaccharide binding protein -

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Basic information

Entry
Database: PDB / ID: 7ehp
TitleChitin oligosaccharide binding protein
Componentschitin oligosaccahride binding protein NagB1
KeywordsSUGAR BINDING PROTEIN / chitin oligosaccahride
Biological speciesPaenibacillus sp. FPU-7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 oligosaccahride binding protein NagB1
B: chitin oligosaccahride binding protein NagB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6264
Polymers91,7772
Non-polymers8492
Water11,403633
1
A: chitin oligosaccahride binding protein NagB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3132
Polymers45,8881
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chitin oligosaccahride binding protein NagB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3132
Polymers45,8881
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.965, 49.798, 77.865
Angle α, β, γ (deg.)90.000, 107.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-699-

HOH

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Components

#1: Protein chitin oligosaccahride binding protein NagB1


Mass: 45888.492 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: 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.: 2
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
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG4000, sodium acetate, Tris

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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: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 47871 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.1 Å2 / Rpim(I) all: 0.099 / Rrim(I) all: 0.214 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.6 % / Num. unique obs: 2402 / CC1/2: 0.642 / Rpim(I) all: 0.511 / Rrim(I) all: 1.098 / % possible all: 100

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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: MOLECULAR REPLACEMENT
Starting model: 7EHO

7eho


Resolution: 2.01→38.93 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 2412 5.04 %
Rwork0.1751 45431 -
obs0.1777 47843 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.85 Å2 / Biso mean: 25.7944 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 2.01→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 58 633 6917
Biso mean--15.69 30.19 -
Num. residues----790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.050.32671030.23592206230982
2.05-2.090.30821640.22926672831100
2.09-2.140.29431370.219326712808100
2.14-2.190.28721710.202126552826100
2.19-2.250.25661470.209427032850100
2.25-2.320.30131200.210926692789100
2.32-2.390.27461350.200527152850100
2.39-2.480.25351520.190126932845100
2.48-2.580.23821500.178126892839100
2.58-2.70.2371230.181826972820100
2.7-2.840.24121440.181626782822100
2.84-3.020.19551310.185327362867100
3.02-3.250.25961440.181627092853100
3.25-3.580.19661440.15792697284199
3.58-4.090.19381510.14072719287099
4.09-5.150.17691430.13842728287199
5.16-38.930.16791530.16362799295299

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