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- PDB-7znw: Artificial Unspecific Peroxygenase expressed in Escherichia coli ... -

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Basic information

Entry
Database: PDB / ID: 7znw
TitleArtificial Unspecific Peroxygenase expressed in Escherichia coli at 2.09 Angstrom resolution
Componentsartificial unspecific peoxygenase
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: 2.09 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: artificial unspecific peoxygenase
C: artificial unspecific peoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2356
Polymers52,9532
Non-polymers1,2824
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-90 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.034, 58.808, 151.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 6 - 238 / Label seq-ID: 6 - 238

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

#1: Protein artificial unspecific peoxygenase


Mass: 26476.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marasmius rotula (fungus) / Production host: Escherichia coli (E. coli) / References: unspecific peroxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES pH 7.5; 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.09→39.34 Å / Num. obs: 25200 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 2.09→2.15 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1910 / CC1/2: 0.94 / Rpim(I) all: 0.32 / % 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: 2.09→38.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.827 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1251 5 %RANDOM
Rwork0.1893 ---
obs0.1916 23891 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.08 Å2 / Biso mean: 30.762 Å2 / Biso min: 17.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--3.02 Å2-0 Å2
3----2.4 Å2
Refinement stepCycle: final / Resolution: 2.09→38.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 88 159 3860
Biso mean--26.9 31.07 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133811
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153467
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.695241
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5967984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1925467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52123.402194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35715560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2241520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024423
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02885
Refine LS restraints NCS

Ens-ID: 1 / Number: 7857 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 2.09→2.144 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 69 -
Rwork0.253 1747 -
all-1816 -
obs--100 %

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