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- PDB-4pwb: Phl p 4 I153V variant, a glucose oxidase, pressurized with Xenon -

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Basic information

Entry
Database: PDB / ID: 4pwb
TitlePhl p 4 I153V variant, a glucose oxidase, pressurized with Xenon
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
FLAVIN-ADENINE DINUCLEOTIDE / MALONATE ION / XENON / Pollen allergen Phl p 4.0202
Similarity search - Component
Biological speciesPhleum pratense (timothy grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.5Sep 2, 2015Group: Database references
Revision 1.6Sep 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)57,0158
Polymers55,7171
Non-polymers1,2987
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.640, 117.640, 202.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

21A-1008-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pollen allergen Phl p 4.0202


Mass: 55716.680 Da / Num. of mol.: 1 / Fragment: Phl p 4.0202 / Mutation: I153V 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

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Non-polymers , 5 types, 384 molecules

#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-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.64 Å3/Da / Density % sol: 66.19 %
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 and pressurized with xenon before freezing, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 11, 2013
RadiationMonochromator: fixed wavelength monochromatic beamline / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 123835 / Num. obs: 123815 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.8 % / Net I/σ(I): 19.32
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 1.27 / Num. unique all: 17659 / % possible all: 100

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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: 1.9→49.407 Å / SU ML: 0.21 / σ(F): 1.91 / Phase error: 18.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 3294 5.03 %random
Rwork0.1597 ---
obs0.1611 123808 99.98 %-
all-123835 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→49.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 71 377 4299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124102
X-RAY DIFFRACTIONf_angle_d1.3415583
X-RAY DIFFRACTIONf_dihedral_angle_d14.3651509
X-RAY DIFFRACTIONf_chiral_restr0.055595
X-RAY DIFFRACTIONf_plane_restr0.007712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.3172080.29973951X-RAY DIFFRACTION100
1.9216-1.94420.28512040.28753878X-RAY DIFFRACTION100
1.9442-1.96790.32312100.27473928X-RAY DIFFRACTION100
1.9679-1.99280.30642080.26563935X-RAY DIFFRACTION100
1.9928-2.0190.24122020.25143936X-RAY DIFFRACTION100
2.019-2.04670.2712060.23913869X-RAY DIFFRACTION100
2.0467-2.07590.24532080.22083938X-RAY DIFFRACTION100
2.0759-2.10690.23092080.21213898X-RAY DIFFRACTION100
2.1069-2.13990.22822130.2163935X-RAY DIFFRACTION100
2.1399-2.17490.25672100.19853948X-RAY DIFFRACTION100
2.1749-2.21240.22632040.1963924X-RAY DIFFRACTION100
2.2124-2.25270.20082050.18173887X-RAY DIFFRACTION100
2.2527-2.2960.19752060.16723925X-RAY DIFFRACTION100
2.296-2.34290.19832060.16383923X-RAY DIFFRACTION100
2.3429-2.39380.19182090.16193922X-RAY DIFFRACTION100
2.3938-2.44950.1822080.15633944X-RAY DIFFRACTION100
2.4495-2.51070.17672040.15433894X-RAY DIFFRACTION100
2.5107-2.57860.19532080.15683912X-RAY DIFFRACTION100
2.5786-2.65450.19872090.15463910X-RAY DIFFRACTION100
2.6545-2.74020.2022070.15483915X-RAY DIFFRACTION100
2.7402-2.83810.20172090.15983915X-RAY DIFFRACTION100
2.8381-2.95170.19232050.15133938X-RAY DIFFRACTION100
2.9517-3.0860.21092080.15513922X-RAY DIFFRACTION100
3.086-3.24870.19472100.15063900X-RAY DIFFRACTION100
3.2487-3.45220.16872100.14523954X-RAY DIFFRACTION100
3.4522-3.71870.16242090.13583892X-RAY DIFFRACTION100
3.7187-4.09270.15912050.1223922X-RAY DIFFRACTION100
4.0927-4.68460.11812080.10143926X-RAY DIFFRACTION100
4.6846-5.90050.12532140.11733923X-RAY DIFFRACTION100
5.9005-49.42390.14682050.15083918X-RAY DIFFRACTION100

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