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- PDB-8j3y: Crystal structure of CBM6E E168Q in complex with oligosaccharides -

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Basic information

Entry
Database: PDB / ID: 8j3y
TitleCrystal structure of CBM6E E168Q in complex with oligosaccharides
ComponentsPutative polysaccharide-binding protein
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


fungal-type cell wall polysaccharide metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
: / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / Putative polysaccharide-binding protein
Similarity search - Component
Biological speciesSaccharophagus degradans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsHe, C. / Li, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biotechnol Biofuels Bioprod / Year: 2024
Title: Structural insights into curdlan degradation via a glycoside hydrolase containing a disruptive carbohydrate-binding module.
Authors: Lv, T. / Feng, J. / Jia, X. / Wang, C. / Li, F. / Peng, H. / Xiao, Y. / Liu, L. / He, C.
History
DepositionApr 18, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative polysaccharide-binding protein
B: Putative polysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,44212
Polymers89,1082
Non-polymers3,33410
Water23,9961332
1
A: Putative polysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4387
Polymers44,5541
Non-polymers1,8846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint0 kcal/mol
Surface area15880 Å2
MethodPISA
2
B: Putative polysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0045
Polymers44,5541
Non-polymers1,4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint0 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.479, 97.802, 72.421
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative polysaccharide-binding protein


Mass: 44554.020 Da / Num. of mol.: 2 / Mutation: E168Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024) (bacteria)
Gene: cbm6E, Sde_1445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21KS2

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Sugars , 3 types, 5 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1337 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1332 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M bis-tris, pH 6.5, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.28→40 Å / Num. obs: 215191 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 0.91 / Net I/σ(I): 6 / Num. measured all: 1428606
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.28-1.36.40.759107210.7570.9280.3260.8280.82100
1.3-1.336.20.659107730.7740.9340.290.7230.824100
1.33-1.356.30.587107050.8330.9530.2540.6410.842100
1.35-1.386.70.533107250.8630.9620.2240.5790.876100
1.38-1.416.80.466107100.8990.9730.1950.5060.886100
1.41-1.446.70.406107460.9170.9780.170.4410.899100
1.44-1.486.60.344107910.9340.9830.1450.3740.934100
1.48-1.526.40.283106660.9530.9880.1210.3090.979100
1.52-1.566.30.243107280.9620.990.1050.2651.007100
1.56-1.616.60.208107460.9710.9930.0880.2271.036100
1.61-1.676.90.177107930.9810.9950.0730.1911.074100
1.67-1.746.80.151107340.9840.9960.0630.1641.088100
1.74-1.826.80.125107890.9890.9970.0520.1361.095100
1.82-1.916.40.102107440.9910.9980.0430.1111.1100
1.91-2.036.60.082107350.9940.9980.0340.0891.139100
2.03-2.197.10.068107720.9960.9990.0270.0731.048100
2.19-2.4170.055107680.9970.9990.0230.060.893100
2.41-2.766.50.044108140.9980.9990.0190.0480.712100
2.76-3.4770.032108360.99910.0130.0340.57100
3.47-406.70.024108950.99910.010.0260.38399.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→21.15 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 10095 4.94 %
Rwork0.1494 --
obs0.1503 204336 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→21.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 224 1332 7834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056824
X-RAY DIFFRACTIONf_angle_d0.8539325
X-RAY DIFFRACTIONf_dihedral_angle_d11.9962332
X-RAY DIFFRACTIONf_chiral_restr0.0811010
X-RAY DIFFRACTIONf_plane_restr0.0081191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.290.23292220.22324163X-RAY DIFFRACTION60
1.29-1.310.24822540.21934819X-RAY DIFFRACTION72
1.31-1.330.22622850.2095351X-RAY DIFFRACTION78
1.33-1.340.23222800.19625646X-RAY DIFFRACTION83
1.34-1.360.20442920.19445789X-RAY DIFFRACTION85
1.36-1.380.22763070.19186212X-RAY DIFFRACTION91
1.38-1.40.20653470.19586406X-RAY DIFFRACTION94
1.4-1.420.20823750.18716556X-RAY DIFFRACTION96
1.42-1.440.20863030.18036629X-RAY DIFFRACTION97
1.44-1.460.18873240.17486620X-RAY DIFFRACTION98
1.46-1.490.17633460.16526701X-RAY DIFFRACTION98
1.49-1.520.17413580.15936747X-RAY DIFFRACTION99
1.52-1.550.18123400.15476797X-RAY DIFFRACTION99
1.55-1.580.17573550.14836760X-RAY DIFFRACTION99
1.58-1.610.1523710.14786678X-RAY DIFFRACTION99
1.61-1.650.16083570.14736785X-RAY DIFFRACTION100
1.65-1.690.16323430.14776822X-RAY DIFFRACTION99
1.69-1.740.16043320.14746784X-RAY DIFFRACTION100
1.74-1.790.15583540.14986763X-RAY DIFFRACTION100
1.79-1.850.17743510.15086837X-RAY DIFFRACTION100
1.85-1.910.16553750.15166785X-RAY DIFFRACTION100
1.91-1.990.18123400.14846819X-RAY DIFFRACTION100
1.99-2.080.16483760.14646788X-RAY DIFFRACTION100
2.08-2.190.16883610.14276807X-RAY DIFFRACTION100
2.19-2.320.173500.14456818X-RAY DIFFRACTION100
2.32-2.50.18053440.15086860X-RAY DIFFRACTION100
2.5-2.760.17983490.15446849X-RAY DIFFRACTION100
2.76-3.150.16963710.15066852X-RAY DIFFRACTION100
3.15-3.970.14083820.12756844X-RAY DIFFRACTION100
3.97-21.150.15223510.14046954X-RAY DIFFRACTION100

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