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- PDB-6f74: Crystal structure of VAO-type flavoprotein MtVAO713 from Myceliop... -

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Basic information

Entry
Database: PDB / ID: 6f74
TitleCrystal structure of VAO-type flavoprotein MtVAO713 from Myceliophthora thermophila C1
ComponentsAlcohol oxidase
KeywordsFLAVOPROTEIN / VAO-type / FAD
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Oxygen oxidoreductase covalent FAD-binding site / Berberine/berberine-like / Berberine and berberine like / Oxygen oxidoreductases covalent FAD-binding site. / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Alcohol oxidase
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
CitationJournal: Molecules / Year: 2018
Title: Characterization of Two VAO-Type Flavoprotein Oxidases from Myceliophthora thermophila.
Authors: Ferrari, A.R. / Rozeboom, H.J. / Vugts, A.S.C. / Koetsier, M.J. / Floor, R. / Fraaije, M.W.
History
DepositionDec 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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 / 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 / _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 2.1May 1, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,76724
Polymers261,3054
Non-polymers6,46120
Water27,4011521
1
A: Alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9426
Polymers65,3261
Non-polymers1,6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8505
Polymers65,3261
Non-polymers1,5234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9426
Polymers65,3261
Non-polymers1,6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0347
Polymers65,3261
Non-polymers1,7076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.195, 108.506, 135.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYSAA27 - 59827 - 598
21THRTHRLYSLYSBB27 - 59827 - 598
12PROPROARGARGAA28 - 59728 - 597
22PROPROARGARGCC28 - 59728 - 597
13THRTHRLYSLYSAA27 - 59827 - 598
23THRTHRLYSLYSDD27 - 59827 - 598
14PROPROARGARGBB28 - 59728 - 597
24PROPROARGARGCC28 - 59728 - 597
15THRTHRLYSLYSBB27 - 59827 - 598
25THRTHRLYSLYSDD27 - 59827 - 598
16PROPROARGARGCC28 - 59728 - 597
26PROPROARGARGDD28 - 59728 - 597

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol oxidase


Mass: 65326.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: First 18 residues are a signal sequence
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Gene: MYCTH_2309690
Production host: Myceliophthora thermophila ATCC 42464 (fungus)
References: UniProt: G2QMS8

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Sugars , 2 types, 8 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.: 4
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.: 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 , 3 types, 1533 molecules

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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1521 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.1 M Tris pH 8.5-9.0 / PH range: 8.5-9.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.574 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 3, 2015
RadiationMonochromator: Helios MX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.574 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.787
11-h,-k,l20.213
ReflectionResolution: 2.2→54.3 Å / Num. obs: 120921 / % possible obs: 98.8 % / Redundancy: 2.1 % / CC1/2: 0.968 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.114 / Net I/σ(I): 3.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5895 / CC1/2: 0.532 / Rpim(I) all: 0.479 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MtVAO615

Resolution: 2.2→54.25 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.885 / SU B: 6.52 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23859 5894 4.9 %RANDOM
Rwork0.19585 ---
obs0.19793 114990 98.58 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1--5.14 Å2-0 Å24.8 Å2
2--23.4 Å20 Å2
3----18.27 Å2
Refinement stepCycle: 1 / Resolution: 2.2→54.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17597 0 428 1522 19547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01918549
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216430
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.96525277
X-RAY DIFFRACTIONr_angle_other_deg1.009338205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1452283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30723.902820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.429152779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.32515100
X-RAY DIFFRACTIONr_chiral_restr0.0870.22690
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120800
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023844
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_it0.0420.1019144
X-RAY DIFFRACTIONr_mcbond_other0.0420.1019143
X-RAY DIFFRACTIONr_mcangle_it0.0780.15111423
X-RAY DIFFRACTIONr_mcangle_other0.0780.15111424
X-RAY DIFFRACTIONr_scbond_it0.3250.1589405
X-RAY DIFFRACTIONr_scbond_other0.3250.1589405
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5440.23313855
X-RAY DIFFRACTIONr_long_range_B_refined3.5712.03521930
X-RAY DIFFRACTIONr_long_range_B_other3.4691.73521672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A375400.05
12B375400.05
21A375900.05
22C375900.05
31A378280.05
32D378280.05
41B375940.04
42C375940.04
51B376300.05
52D376300.05
61C374820.05
62D374820.05
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 459 -
Rwork0.234 8287 -
obs--96.67 %
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)
10.3462-0.04260.17660.1746-0.23111.4646-0.0406-0.0698-0.00480.01750.0101-0.0066-0.0951-0.0740.03050.25840.0017-0.00930.1482-0.00370.2346-11.41338.509118.072
20.61780.10560.01640.46020.23071.0508-0.0010.0261-0.0233-0.0099-0.00580.01660.0223-0.06720.00680.18970.004-0.01930.00580.00220.207721.94438.83563.845
30.44040.1683-0.01980.4168-0.25961.85780.0384-0.06240.0310.028-0.0406-0.01050.04010.0160.00220.24640.0132-0.01740.0967-0.00020.238930.50637.722131.784
40.6111-0.0576-0.08680.34250.19270.80440.00140.0710.0446-0.0229-0.01440.0049-0.0611-0.03990.0130.1871-0.0063-0.02260.01030.01550.2047-19.40238.05150.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 598
2X-RAY DIFFRACTION2B27 - 598
3X-RAY DIFFRACTION3C28 - 598
4X-RAY DIFFRACTION4D27 - 598

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