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- PDB-3lsk: Pyranose 2-oxidase T169S acetate complex -

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Basic information

Entry
Database: PDB / ID: 3lsk
TitlePyranose 2-oxidase T169S acetate complex
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC oxidoreductase / T169S mutant / acetate complex / closed state / Rossmann fold / PHBH fold / homotetramer / covalently bound 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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)284,25718
Polymers277,5994
Non-polymers6,65814
Water34,3911909
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26360 Å2
ΔGint-135 kcal/mol
Surface area80660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.256, 102.454, 136.716
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyranose 2-oxidase / Pyranose oxidase


Mass: 69399.758 Da / Num. of mol.: 4 / Mutation: T169S
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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1909 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 0.1M sodium acetate, 0.05M MgCl2, 6% (w/v)% monomethylether PEG 2000, pH 4.6, 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: 1.038
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2009 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 1.95→38.7 Å / Num. obs: 198647 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.158 / Net I/σ(I): 6.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.772 / % possible all: 99.3

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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: 1.95→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.865 / SU B: 9.442 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2008 1 %RANDOM
Rwork0.196 ---
obs0.196 196612 98.8 %-
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: 9.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20.54 Å2
2--0.54 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18139 0 313 1909 20361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02218919
X-RAY DIFFRACTIONr_bond_other_d00.0216474
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.96125683
X-RAY DIFFRACTIONr_angle_other_deg4.095338467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45352289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97824.477898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.445153029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.75415108
X-RAY DIFFRACTIONr_chiral_restr0.1390.22786
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02120891
X-RAY DIFFRACTIONr_gen_planes_other00.023769
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_it1.0491.511502
X-RAY DIFFRACTIONr_mcbond_other0.3351.54622
X-RAY DIFFRACTIONr_mcangle_it1.678218671
X-RAY DIFFRACTIONr_scbond_it2.69437417
X-RAY DIFFRACTIONr_scangle_it4.0534.57012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.06 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 320 -
Rwork0.242 28694 -
obs--99.32 %
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)
10.2250.01440.05570.20360.06240.2361-0.0053-0.02560.03330.01180.0057-0.0482-0.0161-0.0173-0.00040.0797-0.0014-0.03040.0064-0.00120.075126.37651.178129.286
20.9019-0.04940.26181.59370.22610.65240.0153-0.0187-0.14850.14070.0586-0.22730.10530.0491-0.07380.05940-0.03730.0211-0.01040.125949.87536.832119.344
30.275-0.1549-0.15730.35740.20060.4620.0113-0.00140.08320.01410.0178-0.0385-0.0564-0.0052-0.0290.0632-0.0027-0.03720.00250.00260.085526.39259.101122.723
40.17270.0113-0.03650.2049-0.05840.2925-0.0095-0.0208-0.03350.035-0.004-0.0240.02570.00270.01350.0889-0.0036-0.03970.0120.00010.056920.19618.172133.103
51.0296-1.02230.02641.3912-0.22020.57010.0010.02380.00360.02650.01230.057-0.0413-0.0463-0.01330.0802-0.0057-0.0190.04310.00560.0556-7.81833.753120.769
60.2295-0.05010.15730.2681-0.13550.30950.01880.0065-0.0405-0.001-0.0184-0.04170.04730.0061-0.00040.0809-0.0053-0.03080.00670.00070.05317.70210.398126.983
70.208-0.01110.01610.28910.12830.40280.01460.0851-0.0268-0.0931-0.0351-0.0025-0.0151-0.04820.02050.10670.0061-0.03290.1045-0.01240.02093.91427.89677.806
80.8751-0.52140.30561.22220.07310.38540.01650.1011-0.027-0.1403-0.0002-0.10790.08990.0136-0.01640.1304-0.0127-0.00120.051-0.03490.051513.8165.15589.012
90.3105-0.1550.25230.299-0.08220.7241-0.00270.0897-0.0271-0.0748-0.03450.0431-0.0398-0.10750.03710.0898-0.0022-0.04480.0922-0.02240.0287-4.629.64683.362
100.3840.0148-0.01730.3650.00050.30120.00720.1773-0.0259-0.1346-0.0128-0.11740.01420.05390.00550.09610.01410.03730.1202-0.01170.041737.08331.71575.127
112.2976-1.42890.43871.694-0.32750.7639-0.05710.15830.073-0.0752-0.0024-0.0185-0.1236-0.07790.05940.1469-0.0118-0.01030.10510.04140.031724.20761.03784.82
120.378-0.116-0.05530.50690.11050.3619-0.01530.1362-0.0418-0.0855-0.0006-0.15890.02230.08220.0160.0784-0.00150.04020.0927-0.00970.077744.93133.0681.075
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 388
2X-RAY DIFFRACTION2A389 - 461
3X-RAY DIFFRACTION3A462 - 618
4X-RAY DIFFRACTION4B43 - 370
5X-RAY DIFFRACTION5B371 - 461
6X-RAY DIFFRACTION6B462 - 618
7X-RAY DIFFRACTION7C45 - 393
8X-RAY DIFFRACTION8C394 - 461
9X-RAY DIFFRACTION9C462 - 619
10X-RAY DIFFRACTION10D45 - 374
11X-RAY DIFFRACTION11D375 - 461
12X-RAY DIFFRACTION12D462 - 618

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