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- PDB-3lsi: Pyranose 2-oxidase T169A, tetragonal -

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Basic information

Entry
Database: PDB / ID: 3lsi
TitlePyranose 2-oxidase T169A, tetragonal
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC oxidoreductase / T169A mutant / Rossmann fold / PHBH fold / homotetramer / non-covalent FAD
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 / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsTan, T.C. / Spadiut, O. / Divne, C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: H-bonding and positive charge at the N5/O4 locus are critical for covalent flavin attachment in trametes pyranose 2-oxidase.
Authors: Tan, T.C. / Pitsawong, W. / Wongnate, T. / Spadiut, O. / Haltrich, D. / Chaiyen, P. / Divne, C.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,3394
Polymers138,7682
Non-polymers1,5712
Water18,0871004
1
A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,6778
Polymers277,5354
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area23180 Å2
ΔGint-147 kcal/mol
Surface area80160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.298, 101.298, 249.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Pyranose 2-oxidase / Pyranose oxidase


Mass: 69383.758 Da / Num. of mol.: 2 / Mutation: T169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes ochracea (fungus) / Gene: p2o / Plasmid: pET21(D+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7ZA32, pyranose oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / 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: 46.72 %
Crystal growTemperature: 298 K / pH: 5.2
Details: 0.1M MES, 0.050M MgCl2, 10% (W/V)% monomethylether PEG 2000, pH 5.2, 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: 1.03908
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2009 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03908 Å / Relative weight: 1
ReflectionResolution: 1.9→29.1 Å / Num. obs: 102585 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.115 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.578 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345data collection
FFTmodel building
CCP4model building
REFMAC5.5.0066refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→29.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.521 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3090 3 %RANDOM
Rwork0.164 ---
obs0.166 99494 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9072 0 106 1004 10182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0229420
X-RAY DIFFRACTIONr_bond_other_d00.028177
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.9612814
X-RAY DIFFRACTIONr_angle_other_deg0.824319117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01951149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38724.489450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.809151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4441554
X-RAY DIFFRACTIONr_chiral_restr0.1520.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110471
X-RAY DIFFRACTIONr_gen_planes_other00.021885
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0581.55751
X-RAY DIFFRACTIONr_mcbond_other0.3451.52308
X-RAY DIFFRACTIONr_mcangle_it1.72329344
X-RAY DIFFRACTIONr_scbond_it2.77133669
X-RAY DIFFRACTIONr_scangle_it4.1964.53470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.252 438 -
Rwork0.2 14306 -
obs--99.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8982-0.26320.17270.94790.04390.61990.05170.0903-0.0022-0.145-0.0381-0.06660.08180.0702-0.01360.0750.01340.01570.0711-0.00080.05242.13315.4-42.688
20.1107-0.14060.09410.1934-0.1170.08140.01340.0092-0.01110.0151-0.01080.01150.01880.008-0.00260.07590.00070.00840.07670.00670.05816.247.032-15.82
30.7152-0.0624-0.01371.5343-0.44631.2225-0.00350.03470.06890.00810.03170.0505-0.1262-0.0757-0.02820.0620.0101-0.00370.09890.00730.0698-14.72626.839-31.692
41.45680.1656-0.04910.9265-0.14090.7313-0.0457-0.00090.02670.01380.03620.0351-0.027-0.09790.00950.07830.0025-0.02740.08780.00830.0692-25.65710.541-22.302
50.59650.2864-0.02160.8921-0.16350.4807-0.02280.1097-0.0798-0.12850.0091-0.10070.06240.06950.01380.06010.02150.01440.0675-0.00090.02156.49715.779-42.411
60.7959-0.0322-0.2030.9804-0.05920.96750.0114-0.03510.06740.0271-0.02-0.1757-0.11620.18950.00860.0361-0.0069-0.00670.07290.01610.069610.74327.499-28.584
70.71760.58260.14160.66680.0740.27320.0324-0.0005-0.0070.0227-0.0230.04850.0337-0.0413-0.00940.050.0013-0.0010.0629-0.00280.0418-29.7981.773-15.485
88.185413.4369-1.783922.116-2.92760.4068-0.25780.0012-0.2382-0.52820.1036-0.3770.06540.01220.15430.2528-0.02850.02130.29030.06770.5043-10.469-0.002-10.663
90.43040.0463-0.14710.3774-0.10610.24870.03330.00220.04590.0268-0.0245-0.0211-0.03140.0323-0.00890.0745-0.0006-0.01520.0739-0.00120.0361-5.04419.051-12.404
100.31330.0696-0.09890.4611-0.36050.9731-0.02250.03110.0267-0.0383-0.006-0.0428-0.0046-0.00990.02850.0640.0111-0.00150.06240.01160.0587-2.05628.265-31.677
111.31720.0738-0.6171.38080.5391.51470.02470.2175-0.0242-0.2559-0.04280.1203-0.1135-0.10970.01810.0860.0136-0.03260.0818-0.02770.0232-2.031-19.358-42.291
120.1621-0.0874-0.10890.15160.1110.10520.0190.0119-0.00920.0077-0.02240.0028-0.0215-0.01060.00350.06830.0014-0.00940.0577-0.0120.0463-6.15-8.588-16.536
130.5448-0.19010.04592.5642-0.25511.577-0.02840.0525-0.1204-0.13380.0117-0.00890.28240.08780.01670.07180.01370.00910.0827-0.02490.069814.854-30.016-29.503
141.20770.31690.17741.05550.16982.5769-0.0258-0.0022-0.053-0.0143-0.0101-0.0650.00930.13250.03580.0370.00690.02490.0672-0.0090.06126.049-14.24-19.893
150.74750.27250.32040.82570.25740.4194-0.02810.16580.0318-0.1469-0.00220.0451-0.03040.02220.03030.08050.0031-0.0140.0829-0.01820.02420.568-16.24-41.179
161.18480.05690.0991.13960.4081.7246-0.01110.053-0.1058-0.033-0.07630.21480.151-0.25250.08740.0408-0.0171-0.02630.0736-0.06030.1104-13.408-26.76-32.341
170.80010.50790.15490.61820.09480.3244-0.0046-0.008-0.0394-0.0019-0.0177-0.035-0.02890.04250.02230.0930.00450.01350.0832-0.0030.057919.747-12.098-11.421
181.10860.8971-0.08321.2518-0.00120.32270.00340.00130.0426-0.0072-0.0344-0.0181-0.05140.06050.0310.0690.00280.00340.07980.01280.025329.642-3.327-15.962
193.35238.2892.965320.50037.33372.628-0.36680.08240.2121-0.87720.20650.5344-0.30810.0630.16030.22330.0338-0.04140.1394-0.01780.340710.05-1.577-10.264
200.42570.10970.05340.31940.12530.3649-0.00560.0474-0.0837-0.0248-0.02350.04220.0422-0.01390.02910.05460.0030.00040.0388-0.01780.0543.401-25.724-20.846
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 85
2X-RAY DIFFRACTION2A86 - 166
3X-RAY DIFFRACTION3A167 - 208
4X-RAY DIFFRACTION4A209 - 252
5X-RAY DIFFRACTION5A253 - 307
6X-RAY DIFFRACTION6A308 - 359
7X-RAY DIFFRACTION7A360 - 455
8X-RAY DIFFRACTION8A456 - 462
9X-RAY DIFFRACTION9A463 - 537
10X-RAY DIFFRACTION10A538 - 618
11X-RAY DIFFRACTION11B43 - 82
12X-RAY DIFFRACTION12B83 - 166
13X-RAY DIFFRACTION13B167 - 206
14X-RAY DIFFRACTION14B207 - 246
15X-RAY DIFFRACTION15B247 - 293
16X-RAY DIFFRACTION16B294 - 349
17X-RAY DIFFRACTION17B350 - 384
18X-RAY DIFFRACTION18B385 - 455
19X-RAY DIFFRACTION19B456 - 462
20X-RAY DIFFRACTION20B463 - 618

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