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- PDB-5k8e: Xylooligosaccharide oxidase from Myceliophthora thermophila C1 -

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Basic information

Entry
Database: PDB / ID: 5k8e
TitleXylooligosaccharide oxidase from Myceliophthora thermophila C1
ComponentsFAD linked oxidase-like protein
KeywordsOXIDOREDUCTASE / FAD / CAZy / oligosaccharide / xylose / xylan
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor / FAD binding / oxidoreductase activity / extracellular region
Similarity search - Function
: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type ...: / Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Xylooligosaccharide oxidase
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsRozeboom, H.J. / Ferrari, A.R. / Fraaije, M.W.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO Netherlands
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Discovery of a Xylooligosaccharide Oxidase from Myceliophthora thermophila C1.
Authors: Ferrari, A.R. / Rozeboom, H.J. / Dobruchowska, J.M. / van Leeuwen, S.S. / Vugts, A.S. / Koetsier, M.J. / Visser, J. / Fraaije, M.W.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD linked oxidase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,14611
Polymers54,3761
Non-polymers2,76910
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint13 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.951, 59.440, 68.693
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FAD linked oxidase-like protein


Mass: 54376.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 16 residues are a signal sequence
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Gene: MYCTH_102971
Production host: Myceliophthora thermophila ATCC 42464 (fungus)
References: UniProt: G2QG48, Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor

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Sugars , 2 types, 5 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 3
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 , 4 types, 376 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15-18% PEG3350, 0.1 M MES buffer, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 9, 2015
RadiationMonochromator: HeliosMX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.93→53.6 Å / Num. obs: 37594 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 11.8
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.4 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZR6 and 3RJ8

1zr6

3rj8


Resolution: 1.93→53.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.801 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19544 1853 4.9 %RANDOM
Rwork0.15882 ---
obs0.16056 35740 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å2-0.51 Å2
2--0.38 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.93→53.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 181 371 4225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193987
X-RAY DIFFRACTIONr_bond_other_d0.0010.023560
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.995453
X-RAY DIFFRACTIONr_angle_other_deg0.76238162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03223.901182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51915550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1331521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02932
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_it0.4711.0261898
X-RAY DIFFRACTIONr_mcbond_other0.4711.0241897
X-RAY DIFFRACTIONr_mcangle_it0.831.5362373
X-RAY DIFFRACTIONr_mcangle_other0.831.5372374
X-RAY DIFFRACTIONr_scbond_it0.9681.2752089
X-RAY DIFFRACTIONr_scbond_other0.9661.2752089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5721.873080
X-RAY DIFFRACTIONr_long_range_B_refined4.98710.0974952
X-RAY DIFFRACTIONr_long_range_B_other4.8079.6554810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.929→1.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 121 -
Rwork0.272 2435 -
obs--91.94 %
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)
11.8587-0.18120.18960.7419-0.57280.80290.0033-0.0722-0.19350.023-0.01640.01790.1080.1290.01310.07240.02740.00380.06680.01460.027360.63893.226352.9263
21.0658-0.37080.4380.4559-0.10760.8036-0.0663-0.1578-0.1160.0940.08220.1431-0.0054-0.1219-0.0160.0372-0.00120.01970.05620.03650.052434.504412.06954.0582
37.1491-1.0131-1.09022.7448-1.06073.26010.34460.5494-0.7148-0.6838-0.02530.21530.4173-0.1954-0.31930.26410.0446-0.01340.11930.03050.224243.3745-4.408952.0433
40.8356-0.24570.16150.82760.18231.0161-0.01330.05840.0018-0.02780.0020.0503-0.0679-0.02130.01120.0455-0.0102-0.01190.0560.01470.041738.186717.214237.8304
53.4812-1.02750.7871.7226-0.13122.8599-0.08660.11620.34970.0004-0.0104-0.1546-0.19110.18590.09690.0497-0.0441-0.01720.040.01690.049157.387724.137947.1485
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 124
2X-RAY DIFFRACTION2A125 - 323
3X-RAY DIFFRACTION3A324 - 338
4X-RAY DIFFRACTION4A339 - 455
5X-RAY DIFFRACTION5A456 - 497

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