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- PDB-8p67: Crystal structure of Thermothelomyces thermophila (double mutant ... -

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Basic information

Entry
Database: PDB / ID: 8p67
TitleCrystal structure of Thermothelomyces thermophila (double mutant EE) in complex with aldotetrauronic acid
ComponentsGH30 family xylanase
KeywordsHYDROLASE / glucuronoxylanase / glucuronic acid / aldotetrauronic acid / GH30_7
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
GH30 family xylanase
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 Patras81704 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
DepositionMay 25, 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 1.2Oct 16, 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)106,31211
Polymers103,4582
Non-polymers2,8559
Water15,475859
1
A: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1066
Polymers51,7291
Non-polymers1,3775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2065
Polymers51,7291
Non-polymers1,4774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.203, 107.129, 87.781
Angle α, β, γ (deg.)90.00, 95.75, 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 thermophilus (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 , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)- ...4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 604.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-1-2/a4-b1_b4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 864 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 1.86 Å3/Da / Density % sol: 33.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Na/K Tartrate, PEG3350

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Data collection

DiffractionMean temperature: 120 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.37→45.66 Å / Num. obs: 156777 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 1.37→1.39 Å / Num. unique obs: 7671 / CC1/2: 0.546

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→45.7 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.234 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18743 7771 5 %RANDOM
Rwork0.16317 ---
obs0.16436 148952 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0.09 Å2
2---0.01 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 1.37→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 191 859 7702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137292
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156481
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.65810000
X-RAY DIFFRACTIONr_angle_other_deg1.521.5914921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54122.225346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.876151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4411541
X-RAY DIFFRACTIONr_chiral_restr0.0780.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028549
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021775
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_it1.2741.6383688
X-RAY DIFFRACTIONr_mcbond_other1.2691.6373687
X-RAY DIFFRACTIONr_mcangle_it1.8522.4564657
X-RAY DIFFRACTIONr_mcangle_other1.8522.4564658
X-RAY DIFFRACTIONr_scbond_it1.9251.8673604
X-RAY DIFFRACTIONr_scbond_other1.9251.8673605
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8522.7275341
X-RAY DIFFRACTIONr_long_range_B_refined4.5320.9388542
X-RAY DIFFRACTIONr_long_range_B_other4.53120.9348541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 558 -
Rwork0.298 10939 -
obs--98.72 %

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