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- PDB-7ncx: Crystal structure of GH30 (double mutant EE) from Thermothelomyce... -

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Basic information

Entry
Database: PDB / ID: 7ncx
TitleCrystal structure of GH30 (double mutant EE) from Thermothelomyces thermophila.
ComponentsGH30 family xylanase
KeywordsHYDROLASE / xylanase / GH30 / subfamily 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
DI(HYDROXYETHYL)ETHER / GH30 family xylanase
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsDimarogona, M. / Nikolaivits, E. / Topakas, E. / Weiss, M. / Feiler, C.G.
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
DepositionJan 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
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

Downloads & links

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Assembly

Deposited unit
AAA: GH30 family xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3457
Polymers51,7291
Non-polymers1,6176
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint29 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.887, 87.315, 107.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein GH30 family xylanase


Mass: 51728.941 Da / Num. of mol.: 1
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, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 519 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.94 Å3/Da / Density % sol: 30.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG1500, TBG buffer

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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: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.36→45.9 Å / Num. obs: 79578 / % possible obs: 99.7 % / Redundancy: 12.1 % / CC1/2: 1 / Net I/σ(I): 19.8
Reflection shellResolution: 1.36→1.38 Å / Num. unique obs: 3715 / CC1/2: 0.539

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KRL

6krl


Resolution: 1.36→43.696 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.093 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1581 4024 5.062 %
Rwork0.1221 75477 -
all0.124 --
obs-79501 99.574 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.389 Å20 Å20 Å2
2---0.823 Å20 Å2
3----0.566 Å2
Refinement stepCycle: LAST / Resolution: 1.36→43.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 107 515 3953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133672
X-RAY DIFFRACTIONr_bond_other_d0.0030.0183167
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6715040
X-RAY DIFFRACTIONr_angle_other_deg1.5451.5977370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2622.171175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50315511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0911521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024245
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02807
X-RAY DIFFRACTIONr_nbd_refined0.2120.2694
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23035
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21811
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2334
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.216
X-RAY DIFFRACTIONr_nbd_other0.2080.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.254
X-RAY DIFFRACTIONr_mcbond_it1.5241.4291855
X-RAY DIFFRACTIONr_mcbond_other1.5231.4281854
X-RAY DIFFRACTIONr_mcangle_it1.9982.1552345
X-RAY DIFFRACTIONr_mcangle_other1.9982.1562346
X-RAY DIFFRACTIONr_scbond_it2.0661.6771817
X-RAY DIFFRACTIONr_scbond_other2.0651.6771817
X-RAY DIFFRACTIONr_scangle_it2.4032.432695
X-RAY DIFFRACTIONr_scangle_other2.4032.432696
X-RAY DIFFRACTIONr_lrange_it3.19418.9664291
X-RAY DIFFRACTIONr_lrange_other3.19318.9724292
X-RAY DIFFRACTIONr_rigid_bond_restr1.89836839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.3950.2642790.2485271X-RAY DIFFRACTION95.3608
1.395-1.4340.2482660.2175382X-RAY DIFFRACTION99.2096
1.434-1.4750.2142860.1755216X-RAY DIFFRACTION99.8729
1.475-1.520.1882650.1365100X-RAY DIFFRACTION99.9627
1.52-1.570.1712830.1194941X-RAY DIFFRACTION99.9809
1.57-1.6250.1662650.1144803X-RAY DIFFRACTION99.9606
1.625-1.6870.1582500.1074628X-RAY DIFFRACTION99.9795
1.687-1.7560.152500.0914426X-RAY DIFFRACTION100
1.756-1.8340.152320.0924280X-RAY DIFFRACTION100
1.834-1.9230.1422280.0874088X-RAY DIFFRACTION100
1.923-2.0270.1282050.093919X-RAY DIFFRACTION99.9515
2.027-2.150.1271810.0983748X-RAY DIFFRACTION100
2.15-2.2980.1461700.0963523X-RAY DIFFRACTION100
2.298-2.4820.1311640.0983247X-RAY DIFFRACTION100
2.482-2.7180.1591610.1133018X-RAY DIFFRACTION99.9686
2.718-3.0390.1681460.1282738X-RAY DIFFRACTION100
3.039-3.5080.1531400.1292437X-RAY DIFFRACTION99.8837
3.508-4.2930.1311080.1212095X-RAY DIFFRACTION99.9093
4.293-6.0590.16870.1451641X-RAY DIFFRACTION100
6.059-43.6960.196580.183976X-RAY DIFFRACTION99.7107

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