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

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Basic information

Entry
Database: PDB / ID: 4mig
TitlePyranose 2-oxidase from Phanerochaete chrysosporium, recombinant wild type
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / HOMOTETRAMER / GMC OXIDOREDUCTASE / ROSSMANN FOLD / PHBH FOLD / PYRANOSE 2-OXIDASE / SUGAR 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
DIHYDROFLAVINE-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: 1.8 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_ref_seq_dif.details
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
B: Pyranose 2-oxidase
C: Pyranose 2-oxidase
D: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,47720
Polymers289,1594
Non-polymers4,31816
Water29,6171644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25490 Å2
ΔGint-190 kcal/mol
Surface area78970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.544, 166.448, 91.844
Angle α, β, γ (deg.)90.00, 106.41, 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: 72289.758 Da / Num. of mol.: 4 / Fragment: PYRANOSE 2-OXIDASE
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-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Sugar
ChemComp-G3F / 3-deoxy-3-fluoro-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
b-D-Glcp3fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1644 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS, 0.1 M MnCl2, 30% (w/v) PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2009 / Details: mirrors
RadiationMonochromator: double-crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.95 Å / Num. all: 235360 / Num. obs: 235360 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.05 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.249 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21427 1514 0.6 %RANDOM
Rwork0.17334 ---
obs0.1736 233846 99.02 %-
all-233846 --
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: 21.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.9 Å2
2---0.43 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18105 0 268 1644 20017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0218992
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212833
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.96525876
X-RAY DIFFRACTIONr_angle_other_deg1.052331233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87852314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01123.853885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.164152986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8815122
X-RAY DIFFRACTIONr_chiral_restr0.1660.22837
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02120937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023863
LS refinement shellResolution: 1.8→1.897 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.294 203 -
Rwork0.255 33592 -
obs--98.62 %
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)
11.75320.04530.33561.1752-0.40162.89650.01020.0798-0.2159-0.0837-0.0513-0.25560.2930.27160.04110.04580.0320.01150.0286-0.00040.0813117.427322.19127.7706
20.31540.00620.32960.0614-0.00840.5675-0.00590.0025-0.0319-0.04340.0025-0.0002-0.03040.00050.00340.0599-0.00020.00290.05230.00430.0465106.796839.614216.895
31.03090.1604-0.08141.4387-0.77381.1538-0.04850.030.0275-0.0103-0.0282-0.1561-0.01610.11110.07670.0053-0.0053-0.00470.0705-0.00440.027127.449142.899417.6336
40.54240.0522-0.22250.5318-0.29790.8725-0.0206-0.0185-0.04270.04750.00770.00690.0493-0.030.0130.04350.007-0.01740.0623-0.01850.0371106.308534.78924.7954
51.5597-0.4734-1.21540.29390.19342.6049-0.06390.1536-0.0971-0.076-0.0614-0.02410.13090.13080.12530.0695-0.01480.0230.09060.01890.0628125.4748.93716.0286
60.3050.0301-0.03660.3757-0.24650.6253-0.0179-0.01160.00320.0159-0.00850.0066-0.0063-0.030.02640.03330.0042-0.00180.0439-0.01030.0175106.064345.042423.1022
72.1483-0.5656-0.03912.20660.05270.58970.0054-0.309-0.15840.29530.00560.01450.1450.0914-0.01090.08380.0174-0.02190.06880.00710.0373125.13957.76145.4865
80.21810.0152-0.00970.6815-0.03750.17260.00740.0183-0.0070.0329-0.0214-0.0769-0.01120.03510.01390.01130.0109-0.00320.0303-0.00080.0376116.253731.6488-4.509
91.7637-0.4586-0.42110.83350.03871.19690.03590.0925-0.1703-0.1146-0.00290.03790.1274-0.0153-0.0330.117-0.0106-0.0090.0089-0.02340.1068101.2165.7883-12.1647
100.9539-0.1062-0.04030.4167-0.09940.43730.0097-0.0134-0.06520.0014-0.0094-0.12560.07510.1412-0.00030.08010.03570.00820.0559-0.01950.0975119.685514.5629-5.5271
112.0253-0.5673-1.6251.28060.58062.68690.0271-0.16080.11730.12260.04090.0307-0.09280.0432-0.0680.0880.0057-0.00090.0592-0.00140.104892.906419.8532-5.1703
120.71-0.07210.0630.3992-0.07270.37740.01580.057-0.0527-0.0438-0.0025-0.0940.05930.11-0.01330.04690.02650.02010.0441-0.01610.0483114.885117.1138-16.5437
132.35730.2329-0.76792.1645-0.73621.09290.01350.25060.3018-0.14740.05340.3534-0.0981-0.2144-0.06690.08110.0065-0.05690.06490.01710.116891.589183.1468-34.0895
140.4409-0.5653-0.07271.3910.08930.05370.00560.02240.02410.001-0.01870.0167-0.00230.00420.01310.0484-0.0089-0.00040.04860.00520.011799.566356.419-23.5516
150.6674-0.2093-0.06030.6037-0.04510.7342-0.0376-0.010.10380.0374-0.0069-0.065-0.10470.04330.04450.0579-0.0219-0.01440.01140.01130.0625103.753180.3327-12.2011
160.49-0.0557-0.1350.5052-0.20591.0121-0.02780.13240.0636-0.1101-0.0242-0.0612-0.04660.04980.0520.059-0.0250.0080.04920.02540.0671105.634675.6098-27.0972
172.7010.7655-0.88481.3774-0.54351.0149-0.09060.0886-0.1348-0.01170.06140.12540.0899-0.14930.02920.1031-0.005-0.00190.0651-0.0070.083595.108970.5531-1.4027
180.451-0.0015-0.06610.4724-0.20040.6882-0.03020.08750.0649-0.0578-0.0165-0.0809-0.04830.09930.04670.035-0.02430.00710.03940.02110.0585112.9973.72-18.6647
192.8338-0.63330.84481.50870.15542.131-0.01690.29350.3554-0.19-0.0182-0.1422-0.26020.14550.03510.0915-0.02450.00480.03840.04040.061471.846868.1958-34.7949
200.37780.04050.32660.14780.00830.5182-0.0060.0032-0.0031-0.00140.0089-0.0436-0.03710.0057-0.00280.0350.00660.00280.0280.00060.031478.914651.0078-21.8841
211.3994-0.7296-0.06591.53250.02171.09720.04530.1286-0.0088-0.1813-0.0148-0.02210.08940.102-0.03050.057-0.01170.01560.0976-0.00990.010286.501444.5946-41.6258
220.8366-0.284-0.1010.4333-0.03440.4564-0.02050.00520.0591-0.00260.01750.048-0.0753-0.02280.0030.0895-0.0179-0.010.083-0.00140.061571.28656.7668-24.9623
232.99110.3322-0.97510.2021-0.26930.86610.1249-0.01990.25350.0119-0.0331-0.0314-0.10120.167-0.09180.0601-0.00570.0210.0886-0.01630.054695.30241.9058-36.0544
240.6372-0.24770.08650.3668-0.05980.3072-0.0123-0.02050.01150.00510.01480.0224-0.0157-0.0141-0.00260.0493-0.0090.00230.05360.00030.03272.882445.3842-23.0648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 72
2X-RAY DIFFRACTION2A73 - 201
3X-RAY DIFFRACTION3A202 - 272
4X-RAY DIFFRACTION4A273 - 415
5X-RAY DIFFRACTION5A416 - 467
6X-RAY DIFFRACTION6A468 - 617
7X-RAY DIFFRACTION7B10 - 69
8X-RAY DIFFRACTION8B70 - 161
9X-RAY DIFFRACTION9B162 - 251
10X-RAY DIFFRACTION10B252 - 419
11X-RAY DIFFRACTION11B420 - 467
12X-RAY DIFFRACTION12B468 - 617
13X-RAY DIFFRACTION13C13 - 70
14X-RAY DIFFRACTION14C71 - 129
15X-RAY DIFFRACTION15C130 - 264
16X-RAY DIFFRACTION16C265 - 419
17X-RAY DIFFRACTION17C420 - 467
18X-RAY DIFFRACTION18C468 - 617
19X-RAY DIFFRACTION19D13 - 71
20X-RAY DIFFRACTION20D72 - 201
21X-RAY DIFFRACTION21D202 - 264
22X-RAY DIFFRACTION22D265 - 415
23X-RAY DIFFRACTION23D416 - 467
24X-RAY DIFFRACTION24D468 - 617

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