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- PDB-8c48: Crystal structure of Thermothelomyces thermophila GH30 (double mu... -

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Basic information

Entry
Database: PDB / ID: 8c48
TitleCrystal structure of Thermothelomyces thermophila GH30 (double mutant EE) in complex with xylopentaose
ComponentsGH30 family xylanase
KeywordsHYDROLASE / gucuronoxylanase / xylobiohydrolase / xylopentaose / complex / CBM domain
Function / homology
Function and homology information


glucosylceramide catabolic process / glucosylceramidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / extracellular region / membrane
Similarity search - Function
Endo-beta-1,6-galactanase-like / O-Glycosyl hydrolase family 30 / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
FLUORIDE ION / GH30 family xylanase
Similarity search - Component
Biological speciesThermothelomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDimarogona, M. / Pentari, C. / Kosinas, C. / Topakas, E.
Funding supportEuropean Union, Greece, 3items
OrganizationGrant numberCountry
iNEXT-Discovery20209European Union
Hellenic Foundation for Research and Innovation (HFRI)328 Greece
University of Patras81074 Greece
CitationJournal: Biotechnol.Bioeng. / Year: 2024
Title: Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan.
Authors: Pentari, C. / Kosinas, C. / Nikolaivits, E. / Dimarogona, M. / Topakas, E.
History
DepositionJan 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH30 family xylanase
B: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,22410
Polymers103,4582
Non-polymers3,7668
Water14,250791
1
A: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5134
Polymers51,7291
Non-polymers2,7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7116
Polymers51,7291
Non-polymers9825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.950, 107.806, 88.241
Angle α, β, γ (deg.)90.00, 95.47, 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 GH30 family xylanase


Mass: 51728.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces (fungus) / Gene: Xyn30A, MYCTH_38558 / Production host: Komagataella pastoris (fungus)
References: UniProt: G2Q1N4, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Sugars , 5 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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.: 1
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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a212h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a212h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 794 molecules

#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sodium fluoride, Sodium bromide, Sodium iodide, Sodium HEPES, MOPS,PEG 500 MME, PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 30, 2022
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.34→45.98 Å / Num. obs: 159903 / % possible obs: 98.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 13.4
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 6.9 % / Num. unique obs: 56330 / CC1/2: 0.394 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→45.98 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.588 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15589 7525 5.1 %RANDOM
Rwork0.12761 ---
obs0.12905 140300 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.789 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å2-0.57 Å2
2---0.95 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.4→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6770 0 253 791 7814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137346
X-RAY DIFFRACTIONr_bond_other_d0.0020.0156477
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.66310080
X-RAY DIFFRACTIONr_angle_other_deg1.4411.59114943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88522.406345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.103151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2911539
X-RAY DIFFRACTIONr_chiral_restr0.1310.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021758
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1862.3253676
X-RAY DIFFRACTIONr_mcbond_other2.1722.3253675
X-RAY DIFFRACTIONr_mcangle_it2.7363.5014615
X-RAY DIFFRACTIONr_mcangle_other2.7363.5014616
X-RAY DIFFRACTIONr_scbond_it2.7322.6033670
X-RAY DIFFRACTIONr_scbond_other2.7322.6033671
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2053.825461
X-RAY DIFFRACTIONr_long_range_B_refined4.00828.9838421
X-RAY DIFFRACTIONr_long_range_B_other3.74428.4018225
X-RAY DIFFRACTIONr_rigid_bond_restr1.809313823
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 509 -
Rwork0.271 10280 -
obs--98.41 %

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