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- PDB-7ztn: Crystal structure of fungal CE16 acetyl xylan esterase -

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Basic information

Entry
Database: PDB / ID: 7ztn
TitleCrystal structure of fungal CE16 acetyl xylan esterase
ComponentsCarbohydrate esterase family 16 protein
KeywordsHYDROLASE / acetyl xylan esterase / fungal / hemicellulose
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds
Similarity search - Function
: / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / THIOCYANATE ION / Carbohydrate esterase family 16 protein
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDimarogona, M. / Kosinas, C. / Pentari, C. / Zerva, A. / Topakas, E.
Funding support Greece, European Union, 2items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)328 Greece
European Union (EU)871037European Union
CitationJournal: Carbohydr Polym / Year: 2024
Title: The role of CE16 exo-deacetylases in hemicellulolytic enzyme mixtures revealed by the biochemical and structural study of the novel TtCE16B esterase.
Authors: Pentari, C. / Zerva, A. / Kosinas, C. / Karampa, P. / Puchart, V. / Dimarogona, M. / Topakas, E.
History
DepositionMay 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 23, 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
B: Carbohydrate esterase family 16 protein
A: Carbohydrate esterase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,56316
Polymers79,0082
Non-polymers2,55614
Water13,331740
1
B: Carbohydrate esterase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4696
Polymers39,5041
Non-polymers9655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbohydrate esterase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,09510
Polymers39,5041
Non-polymers1,5919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.825, 91.825, 162.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Carbohydrate esterase family 16 protein


Mass: 39503.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_40885 / Production host: Komagataella pastoris (fungus) / References: UniProt: G2QL32

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Sugars , 3 types, 6 molecules

#2: 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
#3: 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
#4: 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.: 4
Source method: isolated from a genetically manipulated source
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 , 6 types, 748 molecules

#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#8: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Potassium thiocyanate, Bis Tris propane, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→162.4 Å / Num. obs: 140699 / % possible obs: 100 % / Redundancy: 17 % / CC1/2: 0.99 / Net I/σ(I): 15.5
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 6878 / CC1/2: 0.488

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.45→79.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.354 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17143 4822 3.4 %RANDOM
Rwork0.13949 ---
obs0.14097 135800 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.3 Å2-0 Å2
2---0.61 Å2-0 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 1.45→79.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5085 0 162 740 5987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135528
X-RAY DIFFRACTIONr_bond_other_d0.0020.0154917
X-RAY DIFFRACTIONr_angle_refined_deg1.561.687557
X-RAY DIFFRACTIONr_angle_other_deg1.4921.60711355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39922.655275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76815812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3871525
X-RAY DIFFRACTIONr_chiral_restr0.0790.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026340
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021308
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_it1.5051.3522666
X-RAY DIFFRACTIONr_mcbond_other1.4881.3512663
X-RAY DIFFRACTIONr_mcangle_it1.832.0233349
X-RAY DIFFRACTIONr_mcangle_other1.8362.0243350
X-RAY DIFFRACTIONr_scbond_it1.791.5362862
X-RAY DIFFRACTIONr_scbond_other1.791.5372863
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1882.2424207
X-RAY DIFFRACTIONr_long_range_B_refined2.5318.0286563
X-RAY DIFFRACTIONr_long_range_B_other2.4217.1456400
X-RAY DIFFRACTIONr_rigid_bond_restr2.322310445
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.283 10291 -
obs--99.99 %
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)
11.64710.28220.21350.86390.03080.7765-0.00270.0794-0.1014-0.09140.06370.08020.0586-0.1222-0.0610.1024-0.0208-0.04180.09640.02570.032814.2923-24.6277-30.044
20.60630.2509-0.11661.2812-0.36851.1530.049-0.0847-0.020.1926-0.0068-0.0028-0.0364-0.0029-0.04220.0932-0.0045-0.01770.04920.00240.006732.3515-11.36561.048
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B5 - 502
2X-RAY DIFFRACTION2A9 - 611

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