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- PDB-4h7u: Crystal structure of pyranose dehydrogenase from Agaricus meleagr... -

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Basic information

Entry
Database: PDB / ID: 4h7u
TitleCrystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype
ComponentsPyranose dehydrogenase
KeywordsOXIDOREDUCTASE / pyranose dehydrogenase / flavin adduct / GMC-oxidoreductase family / glycoprotein / Rossmann fold/FAD-linked reductases/Alpha and beta proteins (a+b) / FAD binding / Flavin C(4a) oxygen adduct / Secreted
Function / homology
Function and homology information


pyranose dehydrogenase (acceptor) / pyranose dehydrogenase (acceptor) activity / flavin adenine dinucleotide binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / 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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / 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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FED / PHOSPHATE ION / Pyranose dehydrogenase 1
Similarity search - Component
Biological speciesLeucoagaricus meleagris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTan, T.C. / Spadiut, O. / Divne, C.
CitationJournal: Plos One / Year: 2013
Title: The 1.6 A crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate.
Authors: Tan, T.C. / Spadiut, O. / Wongnate, T. / Sucharitakul, J. / Krondorfer, I. / Sygmund, C. / Haltrich, D. / Chaiyen, P. / Peterbauer, C.K. / Divne, C.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyranose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2935
Polymers64,7491
Non-polymers1,5444
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.938, 74.640, 139.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyranose dehydrogenase


Mass: 64748.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leucoagaricus meleagris (fungus) / Gene: pdh1 / Production host: Komagataella pastoris (fungus) / Strain (production host): CBS 7435
References: UniProt: Q3L245, pyranose dehydrogenase (acceptor)

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Sugars , 2 types, 2 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-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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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, 540 molecules

#3: Chemical ChemComp-FED / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate (non-preferred name)


Mass: 803.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O16P2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM KH2PO4, 5% 2-methyl-2,4-pentanediol, 20% (w/v) polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90772 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2009 / Details: mirrors
RadiationMonochromator: Bent Si (220) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90772 Å / Relative weight: 1
ReflectionResolution: 1.6→48.7 Å / Num. all: 72035 / Num. obs: 72035 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.075 / Net I/σ(I): 16.4
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 11811 / Rsym value: 0.841 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345data collection
BALBESphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBV

2jbv


Resolution: 1.6→48.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.318 / SU ML: 0.063 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20116 2177 3 %RANDOM
Rwork0.17081 ---
all0.17176 69857 --
obs0.17176 69857 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 101 538 5014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024585
X-RAY DIFFRACTIONr_bond_other_d0.0010.023002
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9816258
X-RAY DIFFRACTIONr_angle_other_deg1.63237348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08924.789190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92615703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2571519
X-RAY DIFFRACTIONr_chiral_restr0.150.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
LS refinement shellResolution: 1.6→1.686 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.288 263 -
Rwork0.23 9490 -
obs-9490 99.76 %
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)
10.68850.19180.12421.39310.58571.6221-0.04950.09420.0193-0.2209-0.01450.1056-0.2147-0.15530.0640.07740.0233-0.02750.0444-0.00010.014-0.366837.6722-2.9097
25.89451.07411.1894.1802-0.78296.83920.05390.4307-0.1854-0.3754-0.0940.23440.1559-0.23010.04010.04670.0111-0.00950.0648-0.04690.061-2.579221.40413.9815
30.779-0.22360.06280.28380.14910.36880.02920.0818-0.1039-0.0607-0.01750.00650.01840.0184-0.01170.0291-0.00410.00490.0331-0.00560.037313.488424.616512.9242
40.49630.04880.01850.48090.1240.5189-0.0073-0.06240.04270.0292-0.01290.0568-0.1014-0.07370.02020.03760.01210.0080.0485-0.01410.03993.350837.972128.1152
50.9713-0.01020.10040.52690.29780.9134-0.03070.2078-0.0213-0.16330.0378-0.0634-0.15220.0971-0.00720.0948-0.01710.00530.0551-0.00750.014613.251235.7605-6.1388
60.5366-0.0084-0.16180.32320.01460.5984-0.0247-0.0212-0.0514-0.02330.01340.00310.04180.02810.01120.032-0.00390.00050.041-0.00110.046314.12323.91923.8614
70.51740.1369-0.14090.67760.00990.8607-0.0105-0.1151-0.08020.07090.017-0.07780.04710.1235-0.00650.02040.0115-0.00630.0861-0.00150.053722.676225.017429.4581
80.7750.1402-0.29670.892-0.34421.5226-0.00860.05570.1066-0.13330.0153-0.007-0.24630.0095-0.00670.1104-0.0143-0.0010.0216-0.00050.038113.251644.82527.9671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 51
2X-RAY DIFFRACTION2A52 - 66
3X-RAY DIFFRACTION3A67 - 112
4X-RAY DIFFRACTION4A113 - 226
5X-RAY DIFFRACTION5A227 - 312
6X-RAY DIFFRACTION6A313 - 453
7X-RAY DIFFRACTION7A454 - 524
8X-RAY DIFFRACTION8A525 - 577

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