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- PDB-2f6c: Reaction geometry and thermostability of pyranose 2-oxidase from ... -

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Basic information

Entry
Database: PDB / ID: 2f6c
TitleReaction geometry and thermostability of pyranose 2-oxidase from the white-rot fungus Peniophora sp., Thermostability mutant E542K
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / Flavoprotein / covalent / histidine-bound / lignin degradation / thermostability mutation / D2 tetramer / PHBH fold / GMC oxidoreductase / glutathione-reductase related fold
Function / homology
Function and homology information


pyranose oxidase / pyranose oxidase activity / flavin adenine dinucleotide binding / periplasmic space
Similarity search - Function
Phage tail proteins - 2 layer sandwich fold - #50 / Pyranose 2-oxidase / Phage tail proteins - 2 layer sandwich fold / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Pyranose 2-oxidase
Similarity search - Component
Biological speciesPeniophora sp. SG (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.84 Å
AuthorsBannwarth, M. / Heckmann-Pohl, D.M. / Bastian, S. / Giffhorn, F. / Schulz, G.E.
CitationJournal: Biochemistry / Year: 2006
Title: Reaction Geometry and Thermostable Variant of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp.
Authors: Bannwarth, M. / Heckmann-Pohl, D. / Bastian, S. / Giffhorn, F. / Schulz, G.E.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5994
Polymers66,5131
Non-polymers1,0863
Water10,719595
1
A: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,39416
Polymers266,0514
Non-polymers4,34412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area25470 Å2
ΔGint-108 kcal/mol
Surface area82070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.931, 101.931, 118.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2203-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -y-1, -x-1, -z-1 ; -x-1, -y-1. z and y, x, -z-1

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Components

#1: Protein Pyranose 2-oxidase / P2Ox / Pyranose oxidase / PROD / POD / POx / Pyranose:oxygen 2-oxidoreductase / Glucose 2-oxidase / ...P2Ox / Pyranose oxidase / PROD / POD / POx / Pyranose:oxygen 2-oxidoreductase / Glucose 2-oxidase / FAD-oxidoreductase


Mass: 66512.680 Da / Num. of mol.: 1 / Mutation: E542K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peniophora sp. SG (fungus) / Gene: p2ox, poxSG / Plasmid: pET-24a-(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8J136, pyranose oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES/NaOH, pH=6.0, 19% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2003
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.84→77 Å / Num. all: 54760 / Num. obs: 54750 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.84→1.88 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
APRVdata scaling
EPMRphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.84→76.7 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.188 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 2738 5 %RANDOM
Rwork0.15 ---
obs0.15184 52011 100 %-
all-54750 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.84→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4549 0 73 595 5217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224743
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9656449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5724.464224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82215762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2621527
X-RAY DIFFRACTIONr_chiral_restr0.0940.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023656
X-RAY DIFFRACTIONr_nbd_refined0.1960.22262
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2504
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.2133
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.246
X-RAY DIFFRACTIONr_mcbond_it0.6221.52952
X-RAY DIFFRACTIONr_mcangle_it1.02724689
X-RAY DIFFRACTIONr_scbond_it1.76332035
X-RAY DIFFRACTIONr_scangle_it2.7974.51760
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 201 -
Rwork0.172 3813 -
obs--100 %
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)
11.31080.24210.32491.34610.52911.53960.0898-0.1214-0.00630.1451-0.066-0.00290.044-0.0305-0.0238-0.0258-0.00970.0129-0.0277-0.00620.123-2.35417.64642.502
20.4318-0.39860.21551.0832-0.04840.13930.04280.0763-0.0536-0.0601-0.0029-0.05510.07450.0136-0.0399-0.0093-0.00750.0124-0.02330.00410.14464.7372.83425.372
30.4440.84160.54981.59541.04210.68070.0155-0.03970.0113-0.1889-0.06960.0479-0.0441-0.03610.05410.0389-0.0016-0.01410.0027-0.00730.1616-17.39110.5335.209
40.4799-0.07890.10470.0220.04160.4062-0.0244-0.00080.0453-0.02050.01510.0105-0.06240.03110.0094-0.02620.00310.0008-0.0327-0.01140.10517.2419.2125.242
51.6115-0.4792-0.19032.13450.66261.2966-0.0065-0.05730.17240.11450.038-0.059-0.07680.1219-0.0315-0.0325-0.0157-0.0135-0.0093-0.01660.108617.21826.90232.766
62.12160.704-0.86373.2646-0.37831.891-0.0510.0714-0.0361-0.0534-0.0112-0.39090.07980.09420.0623-0.0670.0044-0.028-0.0026-0.040.142528.58614.93815.465
71.60360.1603-0.70960.56270.48450.926-0.0651-0.1413-0.1710.13550.0676-0.07520.13720.1496-0.0025-0.0010.023-0.0105-0.0266-0.00460.128613.9337.79834.551
83.8631.0193.01033.49232.89715.34330.0771-0.2354-0.150.43080.0779-0.19640.28060.2568-0.1550.0403-0.0070.01130.01810.01360.11230.02912.34550.021
90.6937-0.5885-0.62641.85080.49791.0748-0.0628-0.1012-0.02130.12040.03960.34460.0006-0.00280.0233-0.02270.00250.0318-0.0194-0.00970.1663-14.28923.10539.519
101.4888-0.0764-0.66892.52751.24182.06160.03540.11280.2528-0.1516-0.06530.2487-0.2969-0.24470.03-0.01190.0244-0.0145-0.0195-0.00090.1834-13.02731.13824.336
110.817-0.5352-0.65170.97560.72330.6604-0.05270.04790.00280.0738-0.02030.03060.0366-0.01760.073-0.02540.0044-0.0122-0.0530.00210.08179.01318.31412.36
122.1244-1.66850.64475.66380.52940.8017-0.02270.01650.11920.29020.0651-0.52630.09380.0401-0.0424-0.01420.0285-0.0376-0.03320.01210.149236.987-4.57714.341
131.2808-1.26320.36644.3755-0.34591.0185-0.0340.0028-0.06370.07190.04990.1194-0.017-0.0136-0.0158-0.0429-0.00340.0089-0.0243-0.00080.09618.10716.1616.593
142.1868-3.4859-0.50766.83451.26780.3919-0.0078-0.0254-0.25440.0844-0.02910.47660.03950.00780.037-0.0374-0.00380.0038-0.05270.00840.123413.43810.23711.854
151.74350.434-0.57381.3684-0.26330.86490.07760.12550.12790.01930.00250.1826-0.0691-0.1315-0.0801-0.03170.0079-0.0161-0.0302-0.00110.1325-10.8524.23817.197
161.4718-1.3222-0.60831.29160.74620.67140.01740.0480.028-0.0069-0.0531-0.00810.0151-0.04810.0357-0.0282-0.0009-0.0075-0.03390.00440.089613.92317.8495.417
170.88240.0446-0.27980.69290.7871.48720.0202-0.0220.1608-0.01510.00580.0143-0.136-0.0044-0.026-0.02930.00110.0039-0.0497-0.01450.1485-0.03533.57327.332
180.6886-0.0411-0.42090.66730.31471.16790.0192-0.08210.01830.1145-0.04420.047-0.01390.01180.025-0.0176-0.00840.0049-0.0417-0.02260.11263.06828.39837.71
196.53940.4004-2.70261.89161.48242.80050.0086-0.0763-0.052-0.0345-0.02080.0918-0.02340.09350.0122-0.03810.0043-0.0034-0.0590.00920.09361.21115.83727.906
200.225-0.0286-0.06220.21080.04980.18450.0127-0.01350.01230.034-0.0186-0.01680.0158-0.00210.0058-0.0209-0.0076-0.0037-0.0292-0.00380.13757.28616.00922.769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA43 - 8315 - 55
2X-RAY DIFFRACTION2AA84 - 11656 - 88
3X-RAY DIFFRACTION3AA117 - 15289 - 124
4X-RAY DIFFRACTION4AA153 - 181125 - 153
5X-RAY DIFFRACTION5AA182 - 214154 - 186
6X-RAY DIFFRACTION6AA215 - 239187 - 211
7X-RAY DIFFRACTION7AA240 - 263212 - 235
8X-RAY DIFFRACTION8AA264 - 280236 - 252
9X-RAY DIFFRACTION9AA281 - 320253 - 292
10X-RAY DIFFRACTION10AA321 - 352293 - 324
11X-RAY DIFFRACTION11AA353 - 369325 - 341
12X-RAY DIFFRACTION12AA370 - 429342 - 401
13X-RAY DIFFRACTION13AA430 - 455402 - 427
14X-RAY DIFFRACTION14AA456 - 480428 - 452
15X-RAY DIFFRACTION15AA481 - 509453 - 481
16X-RAY DIFFRACTION16AA510 - 543482 - 515
17X-RAY DIFFRACTION17AA544 - 574516 - 546
18X-RAY DIFFRACTION18AA575 - 619547 - 591
19X-RAY DIFFRACTION19AB1625
20X-RAY DIFFRACTION20AE1628 - 2222

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