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- PDB-6h3g: Alcohol oxidase from Phanerochaete chrysosporium -

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Basic information

Entry
Database: PDB / ID: 6h3g
TitleAlcohol oxidase from Phanerochaete chrysosporium
ComponentsAlcohol oxidase
KeywordsOXIDOREDUCTASE / alcohol oxidase / octamer / FAD-binding domain
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Alcohol oxidase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNguyen, Q.-T. / Romero, E. / Dijkman, W.P. / de Vasconcellos, S.P. / Binda, C. / Mattevi, A. / Fraaije, M.W.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Union635734 Italy
CitationJournal: Biochemistry / Year: 2018
Title: Structure-Based Engineering of Phanerochaete chrysosporium Alcohol Oxidase for Enhanced Oxidative Power toward Glycerol.
Authors: Nguyen, Q.T. / Romero, E. / Dijkman, W.P. / de Vasconcellos, S.P. / Binda, C. / Mattevi, A. / Fraaije, M.W.
History
DepositionJul 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol oxidase
B: Alcohol oxidase
C: Alcohol oxidase
D: Alcohol oxidase
E: Alcohol oxidase
F: Alcohol oxidase
G: Alcohol oxidase
H: Alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)587,80821
Polymers581,0638
Non-polymers6,74513
Water10,341574
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.665, 204.037, 116.520
Angle α, β, γ (deg.)90.00, 105.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEASNASNAA10 - 25010 - 250
21ILEILEASNASNBB10 - 25010 - 250
31ILEILEASNASNCC10 - 25010 - 250
41ILEILEASNASNDD10 - 25010 - 250
51ILEILEASNASNEE10 - 25010 - 250
61ILEILEASNASNFF10 - 25010 - 250
71ILEILEASNASNGG10 - 25010 - 250
81ILEILEASNASNHH10 - 25010 - 250
12GLUGLUALAALAAA259 - 638259 - 638
22GLUGLUALAALABB259 - 638259 - 638
32GLUGLUALAALACC259 - 638259 - 638
42GLUGLUALAALADD259 - 638259 - 638
52GLUGLUALAALAEE259 - 638259 - 638
62GLUGLUALAALAFF259 - 638259 - 638
72GLUGLUALAALAGG259 - 638259 - 638
82GLUGLUALAALAHH259 - 638259 - 638

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.071471, -0.793553, -0.60429), (0.988389, 0.13779, -0.064046), (0.134089, -0.592695, 0.794187)161.79205, 102.95655, 90.55602
3given(0.065673, 0.989258, 0.130594), (-0.786704, 0.131841, -0.603087), (-0.613827, -0.063132, 0.786912)-125.40107, 169.2504, 32.8798
4given(-0.855142, 0.195165, -0.480253), (0.206256, -0.721846, -0.660604), (-0.475595, -0.663965, 0.577026)36.92042, 270.64932, 124.83178
5given(-0.084959, 0.791027, 0.605853), (0.789212, -0.317744, 0.525531), (0.608216, 0.522795, -0.597293)-139.70378, 111.78968, 65.11333
6given(-0.999855, -0.015967, -0.005981), (-0.015505, 0.705561, 0.708479), (-0.007092, 0.708469, -0.705706)24.11522, -23.9562, 57.74958
7given(0.855432, -0.193522, 0.480401), (-0.194079, -0.979757, -0.04909), (0.480176, -0.051242, -0.875674)-15.3044, 254.76338, 162.54674
8given(-0.061092, -0.988033, -0.14163), (-0.989119, 0.040903, 0.141315), (-0.133831, 0.148722, -0.979781)148.09012, 118.57452, 152.97011

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Components

#1: Protein
Alcohol oxidase


Mass: 72632.906 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Gene: aox1 / Production host: Escherichia coli (E. coli) / References: UniProt: T2M2J4
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 14% (w/v) PEG3350 and 0.2 M potassium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9726 Å / Relative weight: 1
ReflectionResolution: 2.6→49.32 Å / Num. obs: 151989 / % possible obs: 97.8 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 1.092 / CC1/2: 0.394

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSA

5hsa


Resolution: 2.6→49.32 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 21.299 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26394 7538 5 %RANDOM
Rwork0.19267 ---
obs0.19618 144412 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.577 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20.63 Å2
2--1.32 Å20 Å2
3----4.22 Å2
Refinement stepCycle: 1 / Resolution: 2.6→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40104 0 454 578 41136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01441613
X-RAY DIFFRACTIONr_bond_other_d0.0010.01736369
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.67756551
X-RAY DIFFRACTIONr_angle_other_deg0.8021.64685507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48955107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41221.922245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.537156772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.56415301
X-RAY DIFFRACTIONr_chiral_restr0.0560.25344
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0247056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027556
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_it2.7285.72820449
X-RAY DIFFRACTIONr_mcbond_other2.7275.72820448
X-RAY DIFFRACTIONr_mcangle_it4.3258.58825549
X-RAY DIFFRACTIONr_mcangle_other4.3258.58825550
X-RAY DIFFRACTIONr_scbond_it2.7795.99321164
X-RAY DIFFRACTIONr_scbond_other2.7795.99321164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5328.8831003
X-RAY DIFFRACTIONr_long_range_B_refined6.95766.21946180
X-RAY DIFFRACTIONr_long_range_B_other6.95766.21946180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 9231 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.350.5
Bmedium positional0.320.5
Cmedium positional0.350.5
Dmedium positional0.340.5
Emedium positional0.330.5
Fmedium positional0.350.5
Gmedium positional0.330.5
Hmedium positional0.330.5
Amedium thermal6.512
Bmedium thermal8.992
Cmedium thermal4.932
Dmedium thermal6.622
Emedium thermal12.862
Fmedium thermal5.822
Gmedium thermal7.242
Hmedium thermal6.112
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 551 -
Rwork0.365 10612 -
obs--97.59 %

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