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- PDB-2f5v: Reaction geometry and thermostability mutant of pyranose 2-oxidas... -

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Basic information

Entry
Database: PDB / ID: 2f5v
TitleReaction geometry and thermostability mutant of pyranose 2-oxidase from the white-rot fungus Peniophora sp.
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / Flavoprotein / Rossmann-fold / PHBH-fold / GMC oxidoreductase / glutathion-reductase related fold / tetramer / D2
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 / beta-D-arabino-hexopyranos-2-ulose / DI(HYDROXYETHYL)ETHER / Pyranose 2-oxidase
Similarity search - Component
Biological speciesPeniophora sp. SG (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBannwarth, M. / Bastian, S. / Heckmann-Pohl, D. / 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 28, 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 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 / diffrn_source / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)67,7775
Polymers66,5131
Non-polymers1,2644
Water14,412800
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)271,10720
Polymers266,0504
Non-polymers5,05616
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 area27210 Å2
ΔGint-104 kcal/mol
Surface area81580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.195, 102.195, 119.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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: 66512.617 Da / Num. of mol.: 1
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: Sugar ChemComp-KBG / beta-D-arabino-hexopyranos-2-ulose / BETA-D-ARABINO-HEXOPYRANOS-2-ULOSE


Type: D-saccharide, beta linking / Mass: 178.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O6

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Non-polymers , 4 types, 803 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


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


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


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / pH: 6
Details: 19 % PEG 6000, MES/NaOH, pH=6.0, 4% n-Propanol additive, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.41→62 Å / Num. obs: 119166 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.058 / Net I/σ(I): 27
Reflection shellResolution: 1.41→1.45 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.38 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.971 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2384 2 %RANDOM
Rwork0.149 ---
obs0.149 116780 100 %-
all-119166 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.41→62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4549 0 85 800 5434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224766
X-RAY DIFFRACTIONr_bond_other_d0.0030.024142
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9696467
X-RAY DIFFRACTIONr_angle_other_deg0.863.0029610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9175576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99924.489225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2615760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4061527
X-RAY DIFFRACTIONr_chiral_restr0.1020.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02941
X-RAY DIFFRACTIONr_nbd_refined0.2130.2957
X-RAY DIFFRACTIONr_nbd_other0.190.24328
X-RAY DIFFRACTIONr_nbtor_refined0.180.22364
X-RAY DIFFRACTIONr_nbtor_other0.090.22659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2555
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.2131
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.258
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2121.53697
X-RAY DIFFRACTIONr_mcbond_other0.2721.51157
X-RAY DIFFRACTIONr_mcangle_it1.45824689
X-RAY DIFFRACTIONr_scbond_it2.33432186
X-RAY DIFFRACTIONr_scangle_it3.244.51778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 138 -
Rwork0.329 6735 -
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)
11.05240.206-0.09650.84360.00870.40180.0683-0.11940.03020.1566-0.01910.06290.01220.0037-0.0492-0.1272-0.01110.0183-0.1571-0.01080.0095-2.35417.64642.502
20.3723-0.19870.03060.58060.08450.07070.00790.0493-0.02690.0134-0.034-0.02110.04410.03750.0261-0.1279-0.00380.0069-0.14960.00020.03384.7372.83425.372
30.28210.40680.17611.10180.38780.1447-0.0063-0.00850.0292-0.1-0.03350.0247-0.01110.00530.0398-0.1158-0.0041-0.0108-0.1235-0.00220.0376-17.39110.5335.209
40.3030.08430.0890.2669-0.05220.4005-0.007-0.00260.00560.0020.00810.0108-0.01930.0328-0.001-0.1584-0.00190.0031-0.1674-0.012-0.0027.2419.2125.242
50.7571-0.2695-0.21931.58390.61511.6350.0011-0.01990.08160.11750.0345-0.0765-0.07410.125-0.0356-0.1613-0.0218-0.0101-0.1352-0.02250.013717.21826.90232.766
61.80551.0818-0.15562.8959-0.36441.2484-0.07870.0915-0.0065-0.0910.0436-0.21130.06970.07210.0351-0.17470.0002-0.0169-0.1423-0.00870.040828.58614.93815.465
72.1357-0.2162-1.18360.39790.36381.453-0.0539-0.108-0.1670.1230.043-0.02940.18120.11370.0109-0.13140.0108-0.0174-0.1608-0.0050.017213.9337.79834.551
82.97840.56850.66792.07081.11932.7340.0563-0.3268-0.14160.39070.0154-0.09090.13670.2294-0.0717-0.0533-0.00690.0095-0.11390.01780.00570.02912.34550.021
91.3362-0.3277-0.50851.46270.54040.56390.0049-0.0885-0.02780.1449-0.02380.2190.0297-0.0280.0189-0.1343-0.00750.042-0.1398-0.01230.0557-14.28923.10539.519
100.92240.1465-0.30321.63680.64291.18960.03970.0490.1478-0.1029-0.04420.2234-0.2284-0.14280.0045-0.12820.0315-0.003-0.1445-0.01260.0733-13.02731.13824.336
110.6754-0.6071-0.27550.9740.30040.33870.02650.05030.0073-0.0037-0.06340.03-0.0135-0.03130.0369-0.18560.0019-0.0062-0.1841-0.0034-0.02539.01318.31412.36
122.3154-1.77150.05465.20980.0190.7479-0.0629-0.04710.10960.28750.0999-0.40440.09550.0692-0.037-0.12360.0205-0.0388-0.1341-0.0040.057936.987-4.57714.341
131.025-0.53630.13883.2871-0.29911.0381-0.0557-0.0053-0.02250.0370.05110.0022-0.0062-0.01670.0046-0.1749-0.00380.001-0.1584-0.0085-0.010818.10716.1616.593
141.0529-1.6874-0.51343.34520.95390.4023-0.0184-0.0169-0.15560.0547-0.02640.25960.02880.00320.0449-0.1678-0.003-0.0065-0.167200.015513.43810.23711.854
151.29230.5945-0.68031.5017-0.76471.01810.02550.06310.1106-0.01750.05290.21010.0174-0.1027-0.0784-0.16650.0037-0.015-0.1588-0.01620.0329-10.8524.23817.197
160.731-0.3723-0.24590.77760.43820.68070.02130.01420.023-0.0185-0.0424-0.0071-0.0034-0.04020.0211-0.17450.0026-0.0046-0.17440.0031-0.02113.92317.8495.417
170.24480.23070.00361.06990.73321.26530.00790.00320.075-0.00350.00460.0881-0.07530.0017-0.0125-0.1647-0.00040.009-0.174-0.01470.0264-0.03533.57327.332
180.4951-0.0526-0.1610.73850.34890.89860.0277-0.07370.04990.1356-0.03030.03770.03770.0080.0025-0.1555-0.01440.0122-0.1727-0.02310.00523.06828.39837.71
192.6433-1.121-1.53260.77820.8421.148-0.00230.0253-0.0848-0.0033-0.0122-0.01310.04940.00690.0145-0.1667-0.00180.0087-0.1788-0.00860.00061.21115.83727.906
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 DIFFRACTION19AC1625

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