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- PDB-3k4j: Pyranose 2-oxidase H450Q mutant -

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Basic information

Entry
Database: PDB / ID: 3k4j
TitlePyranose 2-oxidase H450Q mutant
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC OXIDOREDUCTASE / H450Q 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: 2 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

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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)70,3853
Polymers69,4041
Non-polymers9812
Water5,531307
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)281,53812
Polymers277,6154
Non-polymers3,9238
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 area25270 Å2
ΔGint-127 kcal/mol
Surface area80240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.910, 101.910, 120.470
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: 69403.773 Da / Num. of mol.: 1 / Mutation: H450Q
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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
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: Oct 26, 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: 2→30 Å / Num. all: 43397 / Num. obs: 43397 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rsym value: 0.187 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 5784 / Rsym value: 0.859 / % possible all: 99.9

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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: 2→29.2 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.792 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19956 1990 4.6 %RANDOM
Rwork0.15643 ---
all0.15842 41420 --
obs0.15842 41420 99.89 %-
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: 11.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 65 307 4889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224702
X-RAY DIFFRACTIONr_bond_other_d0.0020.023167
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9636396
X-RAY DIFFRACTIONr_angle_other_deg1.01137715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60624.509224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61815754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4941527
X-RAY DIFFRACTIONr_chiral_restr0.1960.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02940
X-RAY DIFFRACTIONr_nbd_refined0.2240.2929
X-RAY DIFFRACTIONr_nbd_other0.2140.23368
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22320
X-RAY DIFFRACTIONr_nbtor_other0.0930.22353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3931.53649
X-RAY DIFFRACTIONr_mcbond_other0.3031.51146
X-RAY DIFFRACTIONr_mcangle_it1.69424653
X-RAY DIFFRACTIONr_scbond_it2.84332145
X-RAY DIFFRACTIONr_scangle_it3.8714.51743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.227 285 -
Rwork0.152 5906 -
obs--99.98 %
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)
10.10160.0388-0.00950.02070.00960.0307-0.00880.0138-0.01050.00350.0162-0.0154-0.0127-0.0057-0.00740.0301-0.00260.00760.0421-0.00970.023361.752346.627835.8776
20.19330.060500.22460.13030.2249-0.00460.06330.0274-0.03140.00430.0065-0.04930.01630.00030.0317-0.01020.01040.03970.0120.006569.053765.844629.0855
30.3533-0.1498-0.18890.21360.19070.2726-0.02350.0141-0.09020.00290.03010.006-0.01270.0546-0.00660.01460.00440.01240.034-0.02060.042777.190240.569130.3282
41.0383-0.4665-0.09740.2561-0.01770.214-0.00710.04510.0325-0.00910.0067-0.00830.0098-0.03490.00040.01880.0001-0.00720.02930.0110.022852.858279.174246.4249
50.1346-0.0239-0.0430.12270.10110.1809-0.01710.0104-0.03080.00590.0198-0.0229-0.02050.0218-0.00260.0163-0.00480.00910.0424-0.01150.02977.243653.047737.7203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 169
2X-RAY DIFFRACTION2A170 - 286
3X-RAY DIFFRACTION3A287 - 365
4X-RAY DIFFRACTION4A366 - 473
5X-RAY DIFFRACTION5A474 - 618

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