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- PDB-4pwc: Phl p 4 I153V N158H variant, a glucose oxidase, 3.5 M NaBr soak -

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Basic information

Entry
Database: PDB / ID: 4pwc
TitlePhl p 4 I153V N158H variant, a glucose oxidase, 3.5 M NaBr soak
ComponentsPollen allergen Phl p 4.0202
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / BI-COVALENT FLAVINYLATION / ALLERGEN / GLUCOSE OXIDASE / HIGH OXYGEN REACTIVITY / GRASS POLLEN
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain ...Vanillyl-alcohol Oxidase; Chain A, domain 3 - #20 / Berberine/berberine-like / Berberine and berberine like / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / Pollen allergen Phl p 4.0202
Similarity search - Component
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZafred, D. / Keller, W. / Macheroux, P.
CitationJournal: Febs J. / Year: 2015
Title: Rationally engineered flavin-dependent oxidase reveals steric control of dioxygen reduction.
Authors: Zafred, D. / Steiner, B. / Teufelberger, A.R. / Hromic, A. / Karplus, P.A. / Schofield, C.J. / Wallner, S. / Macheroux, P.
History
DepositionMar 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Apr 1, 2015Group: Structure summary
Revision 1.4Apr 22, 2015Group: Other
Revision 1.5Jun 3, 2015Group: Other
Revision 1.6Sep 2, 2015Group: Database references
Revision 1.7Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pollen allergen Phl p 4.0202
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,00672
Polymers55,7411
Non-polymers6,26571
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.220, 117.220, 201.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Pollen allergen Phl p 4.0202


Mass: 55740.723 Da / Num. of mol.: 1 / Fragment: Phl p 4.0202 / Mutation: I153V, N158H, N61Q, N330Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phleum pratense (timothy grass) / Gene: phlp4 / Production host: Komagataella pastoris (fungus) / References: UniProt: B2ZWE9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 68 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.58 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7 mg/mL Protein in 20mM Tris + 70% Tacsimate. Crystals were soaked in 55% Tacsimate 20% Glycerol 3.5 M NaBr before freezing, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.915345 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915345 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 68974 / Num. obs: 68911 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 21.2 % / Net I/σ(I): 1.47
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 1.47 / Num. unique all: 8233 / % possible all: 99.9

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERmrphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3TSH

3tsh


Resolution: 2.3→29.305 Å / SU ML: 0.29 / σ(F): 1.9 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 1848 4.97 %random
Rwork0.1861 ---
obs0.188 68721 99.92 %-
all-68974 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 123 150 4126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094046
X-RAY DIFFRACTIONf_angle_d1.195490
X-RAY DIFFRACTIONf_dihedral_angle_d15.2181462
X-RAY DIFFRACTIONf_chiral_restr0.044585
X-RAY DIFFRACTIONf_plane_restr0.006697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33280.34611280.29722716X-RAY DIFFRACTION100
2.3328-2.36770.28311460.29312716X-RAY DIFFRACTION100
2.3677-2.40460.33041410.27982704X-RAY DIFFRACTION100
2.4046-2.4440.32591470.27342750X-RAY DIFFRACTION100
2.444-2.48620.34391520.2662695X-RAY DIFFRACTION100
2.4862-2.53130.26471360.24862745X-RAY DIFFRACTION100
2.5313-2.580.29851450.24772688X-RAY DIFFRACTION100
2.58-2.63260.21671430.24482716X-RAY DIFFRACTION100
2.6326-2.68980.32911400.2452730X-RAY DIFFRACTION100
2.6898-2.75240.30141450.23762705X-RAY DIFFRACTION100
2.7524-2.82110.30841480.23992727X-RAY DIFFRACTION100
2.8211-2.89740.2611410.22262711X-RAY DIFFRACTION100
2.8974-2.98250.25641480.22862741X-RAY DIFFRACTION100
2.9825-3.07870.31971350.23092737X-RAY DIFFRACTION100
3.0787-3.18860.24381500.21352698X-RAY DIFFRACTION100
3.1886-3.31610.28681260.20322730X-RAY DIFFRACTION100
3.3161-3.46680.21081590.18412703X-RAY DIFFRACTION100
3.4668-3.64930.21351350.17012749X-RAY DIFFRACTION100
3.6493-3.87740.18991440.15332705X-RAY DIFFRACTION100
3.8774-4.1760.18731460.15022725X-RAY DIFFRACTION100
4.176-4.59480.14871360.12842722X-RAY DIFFRACTION100
4.5948-5.25640.17611480.13492734X-RAY DIFFRACTION100
5.2564-6.60990.21851380.17282724X-RAY DIFFRACTION100
6.6099-29.30740.17471390.15792734X-RAY DIFFRACTION100

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