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- PDB-4mih: Pyranose 2-oxidase from Phanerochaete chrysosporium, recombinant ... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4mih
TitlePyranose 2-oxidase from Phanerochaete chrysosporium, recombinant H158A mutant
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / HOMOTETRAMER / GMC OXIDOREDUCTASE / ROSSMANN FOLD / PHBH FOLD / PYRANOSE 2-OXIDASER OXIDOREDUCTASE / FLAVINYLATION / HYPHAE
Function / homology
Function and homology information


pyranose oxidase / pyranose oxidase activity / flavin adenine dinucleotide binding / periplasmic space
Similarity search - Function
Pyranose 2-oxidase / : / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 3-deoxy-3-fluoro-beta-D-glucopyranose / Pyranose 2-oxidase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHassan, N. / Tan, T.C. / Spadiut, O. / Pisanelli, I. / Fusco, L. / Haltrich, D. / Peterbauer, C. / Divne, C.
CitationJournal: FEBS Open Bio / Year: 2013
Title: Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly.
Authors: Hassan, N. / Tan, T.C. / Spadiut, O. / Pisanelli, I. / Fusco, L. / Haltrich, D. / Peterbauer, C.K. / Divne, C.
History
DepositionAug 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 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 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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 2-oxidase
B: Pyranose 2-oxidase
C: Pyranose 2-oxidase
D: Pyranose 2-oxidase
E: Pyranose 2-oxidase
F: Pyranose 2-oxidase
G: Pyranose 2-oxidase
H: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,49724
Polymers554,7558
Non-polymers7,74216
Water13,962775
1
A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
C: Pyranose 2-oxidase
D: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,24812
Polymers277,3784
Non-polymers3,8718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24230 Å2
ΔGint-148 kcal/mol
Surface area78830 Å2
MethodPISA
2
E: Pyranose 2-oxidase
F: Pyranose 2-oxidase
G: Pyranose 2-oxidase
H: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,24812
Polymers277,3784
Non-polymers3,8718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24120 Å2
ΔGint-155 kcal/mol
Surface area78860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.100, 167.099, 168.472
Angle α, β, γ (deg.)90.00, 93.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyranose 2-oxidase / P2O / P2Ox / POD / POx / PROD / Pyranose oxidase / FAD-oxidoreductase / Glucose 2-oxidase / ...P2O / P2Ox / POD / POx / PROD / Pyranose oxidase / FAD-oxidoreductase / Glucose 2-oxidase / Pyranose:oxygen 2-oxidoreductase


Mass: 69344.406 Da / Num. of mol.: 8 / Mutation: H158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: p2o, p2ox, pox / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QWR1, pyranose oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Sugar
ChemComp-G3F / 3-deoxy-3-fluoro-beta-D-glucopyranose / 3-deoxy-3-fluoro-beta-D-glucose / 3-deoxy-3-fluoro-D-glucose / 3-deoxy-3-fluoro-glucose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
b-D-Glcp3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 0.2 M NH4Cl, 15% (w/v) PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04094 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 7, 2011 / Details: mirrors
RadiationMonochromator: bent Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04094 Å / Relative weight: 1
ReflectionResolution: 2.4→48.56 Å / Num. all: 233009 / Num. obs: 233009 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Net I/σ(I): 11.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.7 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.558 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 1500 0.64 %
Rwork0.2054 --
obs0.2058 232946 98.41 %
all-232945 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36504 0 520 775 37799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838040
X-RAY DIFFRACTIONf_angle_d1.16551852
X-RAY DIFFRACTIONf_dihedral_angle_d15.02513956
X-RAY DIFFRACTIONf_chiral_restr0.0785676
X-RAY DIFFRACTIONf_plane_restr0.0066720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.39021370.322520751X-RAY DIFFRACTION97
2.4775-2.5660.35821260.29620886X-RAY DIFFRACTION98
2.566-2.66870.31751410.271820862X-RAY DIFFRACTION98
2.6687-2.79020.31261350.259620893X-RAY DIFFRACTION98
2.7902-2.93730.28471530.24120940X-RAY DIFFRACTION98
2.9373-3.12130.32431470.243221030X-RAY DIFFRACTION99
3.1213-3.36220.29831300.237421061X-RAY DIFFRACTION99
3.3622-3.70050.2741310.212621139X-RAY DIFFRACTION99
3.7005-4.23570.26741270.184321204X-RAY DIFFRACTION99
4.2357-5.33540.22471280.158721254X-RAY DIFFRACTION99
5.3354-48.5680.19171450.161721426X-RAY DIFFRACTION99
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)
10.23420.0316-0.14990.2334-0.16420.1941-0.0457-0.0217-0.12730.03970.0952-0.12740.09970.2782-0.02750.12930.07780.06750.2631-0.16890.3956-32.0748-57.3594-23.2151
20.39430.06180.12930.25740.3610.5087-0.08620.16610.2009-0.214-0.0647-0.007-0.3306-0.0676-0.07760.2586-0.0051-0.00750.1987-0.04290.2117-47.2868-24.6997-31.3008
30.4904-0.1160.1960.21420.10210.23280.07160.0223-0.3045-0.0609-0.02440.13210.0356-0.05210.03660.12290.03220.00870.1324-0.04370.3086-55.7137-58.62-21.8128
40.06370.0306-0.05320.0607-0.00270.2078-0.0024-0.1667-0.18190.06980.01040.09860.15150.0130.0010.1599-0.0043-0.03040.20020.0370.385-46.9842-60.135-11.8336
50.1372-0.06380.00240.0345-0.01160.01570.04360.2049-0.1369-0.1520.0719-0.11420.060.13860.28490.17180.030.12930.4037-0.20630.2754-40.1329-53.8318-39.5895
60.1492-0.0295-0.12940.12750.1110.17320.0044-0.3374-0.15810.29670.026-0.00990.09840.09210.01230.2659-0.0390.06020.27670.09580.2798-57.3109-52.1158.3633
70.11650.0318-0.02840.0832-0.09170.10410.0203-0.12920.03380.03840.0340.0517-0.04080.01650.12250.06410.0110.03540.2206-0.01960.2296-59.6624-49.4242-13.5415
80.2696-0.12180.04360.33520.09870.13430.05470.2168-0.2115-0.15420.0201-0.0519-0.00280.0470.10410.00130.08410.0370.208-0.17510.2358-55.3114-52.6194-30.6526
90.6575-0.12990.04870.11510.33971.37130.0238-0.1563-0.51570.00940.0234-0.04840.4530.1097-0.01550.17750.0869-0.01840.36060.03640.5095-14.5155-47.3375-2.9813
100.6254-0.17950.20030.51230.18550.6319-0.0099-0.00930.0004-0.0748-0.0022-0.2814-0.02710.21420.00990.09820.04360.04960.238-0.03030.3168-25.6847-30.8159-11.4572
111.2147-0.0561-0.04560.93460.14230.3944-0.0761-0.1444-0.014-0.05380.114-0.2166-0.00540.12090.01530.0550.03750.02380.2077-0.0410.2207-27.0186-25.2093-6.4735
120.4062-0.0893-0.2130.16590.05190.1195-0.0473-0.12840.41930.0051-0.07230.2433-0.3236-0.4276-0.05140.44210.3274-0.2560.5537-0.31870.7881-90.0679-3.6543-6.0107
130.25510.03270.01820.06290.0670.1555-0.1155-0.30610.1903-0.0351-0.20480.3434-0.2108-0.3465-0.310.13320.2519-0.10380.5815-0.36410.5832-85.7023-18.7454-2.6104
140.6804-0.03660.05270.38350.09110.3494-0.0327-0.36450.1584-0.0581-0.06680.349-0.1787-0.42590.2254-0.17520.2993-0.02070.4694-0.26170.39-83.1186-23.9167-3.7099
150.4005-0.4698-0.44370.67660.37540.65550.03530.0689-0.15040.036-0.04360.3683-0.0111-0.1948-0.29840.59910.2089-0.26810.34350.02880.7126-85.170413.4358-27.1025
160.0559-0.0213-0.00840.1956-0.08380.2508-0.12420.03690.2531-0.1558-0.04620.0572-0.2086-0.0794-0.26510.45130.1185-0.27540.2361-0.05510.4252-70.3506-4.1621-22.8203
170.1915-0.0420.02810.43610.42070.7546-0.0580.02420.3781-0.25930.0788-0.0978-0.26270.05140.03460.42720.0732-0.19350.1626-0.00410.604-57.143814.7537-14.4663
180.807-0.03250.010.63180.01940.1375-0.01290.14920.3161-0.43840.03420.2736-0.2122-0.0270.00010.49330.103-0.25150.14820.04720.5048-63.13824.5108-25.1675
190.8647-0.0743-0.14670.22540.26740.4357-0.0867-0.2484-0.27780.15650.02480.04110.2897-0.0190.02580.3640.02450.12160.1982-0.02870.1885.626-82.2015-54.0265
200.5021-0.1466-0.15120.6161-0.12460.5966-0.0541-0.143-0.05590.20830.0248-0.03050.0469-0.0330.02090.22260.03080.05030.161-0.050.07446.3261-68.131-51.255
210.11630.07590.07340.1797-0.0620.1434-0.0970.0644-0.00260.0253-0.0203-0.0121-0.1081-0.0383-0.01070.25760.0399-0.02160.1658-0.07670.138811.1513-58.524-57.6207
220.1441-0.12730.07560.21560.05780.1702-0.077-0.0618-0.04470.14270.01040.1425-0.0357-0.14910.27030.26910.0350.10140.185-0.07810.0723-2.7453-63.7118-55.6183
230.3899-0.12290.03640.35150.11680.31-0.0315-0.1272-0.2120.20490.0302-0.19320.16110.08630.00060.3420.0354-0.06960.2077-0.0040.342126.1893-88.4598-61.0093
240.459-0.00370.04130.9055-0.00530.8099-0.0029-0.0563-0.18920.02840.0291-0.29510.17590.06810.00170.30070.0281-0.00060.1712-0.02770.287726.8697-95.9123-72.5089
250.1948-0.0346-0.06940.23960.17680.1870.08810.20080.0915-0.3995-0.0911-0.2329-0.00260.16180.00260.4046-0.07630.10730.36420.05940.461335.8397-43.8407-96.4257
260.59180.0768-0.17140.8127-0.0660.7721-0.02460.10660.2141-0.0740.0293-0.3774-0.24350.16160.00190.3188-0.09560.0160.18750.02940.350730.563-34.3613-84.1363
270.4498-0.13650.13310.25750.13580.193-0.04610.30140.2396-0.33240.0373-0.1032-0.02730.16890.01440.5127-0.09270.02020.34120.08080.22616.9437-51.9934-107.9414
280.42180.0732-0.02830.8266-0.07130.6938-0.11810.34260.063-0.46410.0181-0.21870.01520.1524-0.02250.5081-0.10790.07120.3504-0.02930.10319.9591-64.4583-112.7396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 268 )
5X-RAY DIFFRACTION5chain 'A' and (resid 269 through 395 )
6X-RAY DIFFRACTION6chain 'A' and (resid 396 through 439 )
7X-RAY DIFFRACTION7chain 'A' and (resid 440 through 470 )
8X-RAY DIFFRACTION8chain 'A' and (resid 471 through 617 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 34 )
10X-RAY DIFFRACTION10chain 'B' and (resid 35 through 287 )
11X-RAY DIFFRACTION11chain 'B' and (resid 288 through 617 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 99 )
13X-RAY DIFFRACTION13chain 'C' and (resid 100 through 306 )
14X-RAY DIFFRACTION14chain 'C' and (resid 307 through 617 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 34 )
16X-RAY DIFFRACTION16chain 'D' and (resid 35 through 172 )
17X-RAY DIFFRACTION17chain 'D' and (resid 173 through 263 )
18X-RAY DIFFRACTION18chain 'D' and (resid 264 through 617 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 119 )
20X-RAY DIFFRACTION20chain 'E' and (resid 120 through 439 )
21X-RAY DIFFRACTION21chain 'E' and (resid 440 through 493 )
22X-RAY DIFFRACTION22chain 'E' and (resid 494 through 617 )
23X-RAY DIFFRACTION23chain 'F' and (resid 1 through 172 )
24X-RAY DIFFRACTION24chain 'F' and (resid 173 through 617 )
25X-RAY DIFFRACTION25chain 'G' and (resid 1 through 146 )
26X-RAY DIFFRACTION26chain 'G' and (resid 147 through 617 )
27X-RAY DIFFRACTION27chain 'H' and (resid 1 through 172 )
28X-RAY DIFFRACTION28chain 'H' and (resid 173 through 617 )

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