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- PDB-6f73: Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 fro... -

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Basic information

Entry
Database: PDB / ID: 6f73
TitleCrystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora thermophila C1
ComponentsMtVAO615
KeywordsFLAVOPROTEIN / VAO-type / FAD
Function / homology
Function and homology information


: / secondary metabolite biosynthetic process / FAD binding / oxidoreductase activity / extracellular region
Similarity search - Function
Berberine/berberine-like / Berberine and berberine like / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / VAO-type flavoprotein oxidase VAO615
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 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 2.1Jan 17, 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

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Assembly

Deposited unit
A: MtVAO615
B: MtVAO615
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,01713
Polymers124,0492
Non-polymers3,96811
Water15,205844
1
A: MtVAO615
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6775
Polymers62,0241
Non-polymers1,6524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MtVAO615
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3408
Polymers62,0241
Non-polymers2,3167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.417, 115.959, 198.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 27 - 574 / Label seq-ID: 27 - 574

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein MtVAO615


Mass: 62024.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: First 17 residues are a signal sequence
Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus)
Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2305637
Production host: Myceliophthora thermophila ATCC 42464 (fungus)
References: UniProt: G2QDQ9
#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
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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.: 7
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG6000, , 0.2 M NaCl, 0.1 M NaAcetate pH 5.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 2015
RadiationMonochromator: Helios MX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→58 Å / Num. obs: 71982 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.081 / Net I/σ(I): 12.9
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4265 / CC1/2: 0.706 / Rpim(I) all: 0.225 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IPI, 2BVF, 2Y08, 3W8W,3RJ8

2ipi

2bvf

2y08

3w8w

3rj8


Resolution: 2.22→58 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23467 3610 5 %RANDOM
Rwork0.1928 ---
obs0.19489 68291 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 36.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2--0.46 Å20 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 2.22→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8364 0 260 847 9471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198899
X-RAY DIFFRACTIONr_bond_other_d00.027982
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.96912171
X-RAY DIFFRACTIONr_angle_other_deg3.844318369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96951094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00923.598378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.926151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0021544
X-RAY DIFFRACTIONr_chiral_restr0.0730.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110130
X-RAY DIFFRACTIONr_gen_planes_other0.0290.022100
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_it2.410.6624382
X-RAY DIFFRACTIONr_mcbond_other2.410.6624381
X-RAY DIFFRACTIONr_mcangle_it3.1620.9875474
X-RAY DIFFRACTIONr_mcangle_other3.1610.9875475
X-RAY DIFFRACTIONr_scbond_it5.971.134517
X-RAY DIFFRACTIONr_scbond_other5.9691.134518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1051.566698
X-RAY DIFFRACTIONr_long_range_B_refined9.43110.7110452
X-RAY DIFFRACTIONr_long_range_B_other9.44610.17410299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 35812 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.219→2.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 267 -
Rwork0.285 4669 -
obs--93.52 %
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)
12.985-0.1427-1.40230.84410.3733.3990.0136-0.32540.2440.48840.03260.0127-0.49660.1149-0.04620.5194-0.0028-0.00210.32780.00460.351359.03587.638111.717
20.9097-0.1794-1.22311.7343-0.25414.44220.14890.00930.07350.097-0.0953-0.0505-0.5045-0.2691-0.05370.13130.0256-0.00390.18960.01260.278561.9586.06788.097
36.9888-1.0507-0.84880.23770.33240.70120.55591.7516-0.0588-0.1138-0.54-0.0574-0.22-1.0608-0.01590.22750.3839-0.04971.6614-0.0550.614225.96689.85581.706
42.6133-0.7001-1.32970.65750.38572.42580.21120.9482-0.0174-0.0509-0.34780.3022-0.6911-1.84850.13670.31070.4516-0.03281.4845-0.14260.50434.82888.51681.545
52.0077-0.5551-1.44811.34070.62953.1946-0.08690.3387-0.27860.1111-0.20760.31810.1086-0.95080.29460.1381-0.0570.04740.4559-0.07260.384848.1374.13391.649
61.0877-2.2811-3.09296.37273.489215.1398-0.1908-0.0038-0.2330.2406-0.14040.49310.5479-0.00640.33120.4217-0.09010.05480.43550.14910.420859.20866.692107.308
72.02661.6365-0.31924.191.95539.2855-0.0255-0.0583-0.05020.2456-0.28120.23140.4117-0.43070.30670.1702-0.00890.11010.13920.05860.463843.31831.20860.91
80.806-0.1010.22331.64530.90721.0427-0.12560.132-0.0709-0.09250.03570.18110.12170.00760.08990.1406-0.0440.01020.04390.01720.373253.40539.58548.143
90.4403-0.1272-0.05031.4523-0.23431.1008-0.04450.00860.0691-0.05730.00240.1246-0.0594-0.08110.04210.01390.0046-0.00990.0062-0.00450.32149.97461.37456.352
102.6033-0.77230.49721.0311-0.12590.6686-0.00940.06530.0775-0.13420.0313-0.17280.02320.0885-0.0220.0442-0.00240.02870.01560.00310.363877.30773.24852.499
111.12430.103-0.0251.05290.27350.4583-0.057-0.11820.04480.07750.0472-0.10760.01210.06910.00990.05740.0294-0.00740.03210.01280.287367.21556.33265.295
121.4581-1.0381-2.706813.03465.33955.9838-0.0782-0.11990.070.75030.2299-0.20340.37080.2988-0.15160.28410.05120.01180.14520.06040.338152.91237.99870.318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 140
2X-RAY DIFFRACTION2A141 - 300
3X-RAY DIFFRACTION3A301 - 323
4X-RAY DIFFRACTION4A324 - 447
5X-RAY DIFFRACTION5A448 - 560
6X-RAY DIFFRACTION6A561 - 574
7X-RAY DIFFRACTION7B27 - 41
8X-RAY DIFFRACTION8B42 - 146
9X-RAY DIFFRACTION9B147 - 294
10X-RAY DIFFRACTION10B295 - 398
11X-RAY DIFFRACTION11B399 - 559
12X-RAY DIFFRACTION12B560 - 574

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