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- PDB-7o0e: Crystal structure of GH30 (mutant E188A) complexed with aldotriur... -

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Basic information

Entry
Database: PDB / ID: 7o0e
TitleCrystal structure of GH30 (mutant E188A) complexed with aldotriuronic acid from Thermothelomyces thermophila.
ComponentsGH30 family xylanase
KeywordsHYDROLASE / xylanase / GH30 / subfamily 7 / fungal
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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GLYCINE / DI(HYDROXYETHYL)ETHER / GH30 family xylanase
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDimarogona, M. / Kosinas, C. / Feiler, C. / Weiss, M.S. / Topakas, E. / Nikolaivits, E.
CitationJournal: Carbohydrate Polymers / Year: 2021
Title: Unique features of the bifunctional GH30 from Thermothelomyces thermophila revealed by structural and mutational studies
Authors: Nikolaivits, E. / Pentari, C. / Kosinas, C. / Feiler, C.G. / Spiliopoulou, M. / Weiss, M.S. / Dimarogona, M. / Topakas, E.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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
G: GH30 family xylanase
A: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,87915
Polymers96,4562
Non-polymers2,42313
Water12,304683
1
G: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0507
Polymers48,2281
Non-polymers8226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8308
Polymers48,2281
Non-polymers1,6017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.604, 41.001, 107.786
Angle α, β, γ (deg.)90.000, 91.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules GA

#1: Protein GH30 family xylanase


Mass: 48228.109 Da / Num. of mol.: 2 / Mutation: E188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / 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 , 2 types, 3 molecules

#2: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 472.396 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-2/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 693 molecules

#4: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.02013588 Å3/Da / Density % sol: 39.1508331 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG pH 7.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→46.884 Å / Num. obs: 67654 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 4130 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NCX

7ncx


Resolution: 1.85→46.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.581 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 3293 4.9 %RANDOM
Rwork0.1549 ---
obs0.1566 64342 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.22 Å2 / Biso mean: 21.117 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.08 Å2
2--0.49 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.85→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 162 683 7565
Biso mean--33.57 32.01 -
Num. residues----893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137139
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186194
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6599746
X-RAY DIFFRACTIONr_angle_other_deg1.4151.59414371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3322.232345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.469151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5171541
X-RAY DIFFRACTIONr_chiral_restr0.070.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021551
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 224 -
Rwork0.256 4722 -
all-4946 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.239-0.10260.15180.0755-0.03620.43730.01180.0255-0.0141-0.002-0.03650.00910.00060.0020.02470.02060.0024-0.0290.0256-0.00870.0436-8.4186.93-30.101
20.4495-0.0201-0.09680.01430.05760.46260.0180.0088-0.0228-0.00370.00570.01090.01320.0482-0.02360.0050.0031-0.01130.04460.00680.0308-52.858-6.019-23.986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G8 - 459
2X-RAY DIFFRACTION1G601 - 605
3X-RAY DIFFRACTION2A10 - 457
4X-RAY DIFFRACTION2A601 - 605

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