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- PDB-7znv: Artificial Unspecific Peroxygenase expressed in Pichia pastoris a... -

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Basic information

Entry
Database: PDB / ID: 7znv
TitleArtificial Unspecific Peroxygenase expressed in Pichia pastoris at 1.21 Angstrom resolution
Componentsartificial unspecific peroxygenase
KeywordsOXIDOREDUCTASE / Heme / peroxygenase / UPO
Function / homologyChloroperoxidase / Chloroperoxidase-like / Orthogonal Bundle / Mainly Alpha / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesMarasmius rotula (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsRobinson, W.X.Q. / Mielke, T. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2023
Title: Comparing the Catalytic and Structural Characteristics of a 'Short' Unspecific Peroxygenase (UPO) Expressed in Pichia pastoris and Escherichia coli.
Authors: Robinson, W.X.Q. / Mielke, T. / Melling, B. / Cuetos, A. / Parkin, A. / Unsworth, W.P. / Cartwright, J. / Grogan, G.
History
DepositionApr 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: artificial unspecific peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7635
Polymers26,4761
Non-polymers1,2864
Water6,720373
1
A: artificial unspecific peroxygenase
hetero molecules

A: artificial unspecific peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,52610
Polymers52,9532
Non-polymers2,5738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5600 Å2
ΔGint-71 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.851, 74.168, 154.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-580-

HOH

21A-711-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein artificial unspecific peroxygenase


Mass: 26476.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marasmius rotula (fungus) / Production host: Komagataella pastoris (fungus) / References: unspecific peroxygenase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 375 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.15 M KSCN, 25% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.21→77.27 Å / Num. obs: 89172 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Net I/σ(I): 23.6
Reflection shellResolution: 1.21→1.23 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4348 / CC1/2: 0.92 / Rpim(I) all: 0.28 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FUJ

5fuj


Resolution: 1.21→77.27 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.458 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.165 4405 4.9 %RANDOM
Rwork0.1485 ---
obs0.1494 84702 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.6 Å2 / Biso mean: 14.58 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0 Å2
2---0.08 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 1.21→77.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 86 379 2267
Biso mean--19.8 27.45 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151842
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.7182791
X-RAY DIFFRACTIONr_angle_other_deg1.6251.6234268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96723.762101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74115300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9881510
X-RAY DIFFRACTIONr_chiral_restr0.1240.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022337
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02456
LS refinement shellResolution: 1.21→1.241 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 340 -
Rwork0.211 6169 -
all-6509 -
obs--99.86 %

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