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- PDB-3k4k: Pyranose 2-oxidase F454N mutant -

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Basic information

Entry
Database: PDB / ID: 3k4k
TitlePyranose 2-oxidase F454N mutant
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC OXIDOREDUCTASE / F454N MUTANT / ROSSMANN FOLD / PHBH FOLD / HOMOTETRAMER / 8-ALPHA-(N3) HISTIDYL FLAVINYLATION
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDivne, C. / Tan, T.C.
CitationJournal: Febs J. / Year: 2010
Title: Importance of the gating segment in the substrate-recognition loop of pyranose 2-oxidase.
Authors: Spadiut, O. / Tan, T.C. / Pisanelli, I. / Haltrich, D. / Divne, C.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Oct 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 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1662
Polymers69,3811
Non-polymers7861
Water7,855436
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)280,6658
Polymers277,5234
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area22900 Å2
ΔGint-152 kcal/mol
Surface area81050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.059, 102.059, 119.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Pyranose 2-oxidase / Pyranose oxidase


Mass: 69380.719 Da / Num. of mol.: 1 / Mutation: F454N
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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1M MES, 50MM 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: 1.0379 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2008 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 83548 / Num. obs: 83548 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Rsym value: 0.1 / Net I/σ(I): 18.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 13637 / Rsym value: 0.86 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IGO

2igo


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.099 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 1961 2.3 %RANDOM
Rwork0.18488 ---
all0.18556 81587 --
obs0.18556 81587 99.88 %-
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: 12.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4531 0 53 436 5020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224704
X-RAY DIFFRACTIONr_bond_other_d0.0020.023159
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.966400
X-RAY DIFFRACTIONr_angle_other_deg1.01137697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29124.533225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47415756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2811527
X-RAY DIFFRACTIONr_chiral_restr0.1610.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02939
X-RAY DIFFRACTIONr_nbd_refined0.2350.21005
X-RAY DIFFRACTIONr_nbd_other0.2130.23497
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22381
X-RAY DIFFRACTIONr_nbtor_other0.0920.22434
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2302
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2230.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4261.53634
X-RAY DIFFRACTIONr_mcbond_other0.3631.51150
X-RAY DIFFRACTIONr_mcangle_it1.66324670
X-RAY DIFFRACTIONr_scbond_it2.73932105
X-RAY DIFFRACTIONr_scangle_it3.6994.51730
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.686 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 276 -
Rwork0.215 11672 -
obs--99.54 %
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)
10.07320.0657-0.04440.0951-0.0160.0546-0.00820.0237-0.01750.00210.01370.0059-0.0012-0.0044-0.00550.02320.00790.00510.0605-0.00920.021661.63945.893335.2148
20.16820.0124-0.04180.14860.07120.1256-0.00140.0541-0.0163-0.00250.00340.0026-0.02190.0233-0.0020.0180.00010.00460.0625-0.00270.016471.845855.548429.1273
31.6417-0.95-0.02720.6623-0.03770.08520.00580.12150.13870.0104-0.0089-0.06010.0156-0.02910.00310.01350.0033-0.00440.04530.02880.031453.407381.87645.7498
43.71172.2259-4.49953.3037-2.67615.4548-0.56210.2563-0.7096-0.32330.16030.3280.74160.15150.40180.138-0.02590.02190.14860.01660.150552.131563.290948.3239
50.1237-0.03410.00190.07430.08950.1247-0.00770.0219-0.01480.01730.0175-0.0131-0.01780.026-0.00990.0197-0.00150.00670.0563-0.00240.030375.595754.426938.4024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 151
2X-RAY DIFFRACTION2A152 - 359
3X-RAY DIFFRACTION3A360 - 449
4X-RAY DIFFRACTION4A450 - 462
5X-RAY DIFFRACTION5A463 - 618

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