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- PDB-6ekx: Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita... -

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Basic information

Entry
Database: PDB / ID: 6ekx
TitleDirect-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with 1-naphthol (I)
ComponentsAromatic peroxygenase
KeywordsOXIDOREDUCTASE / directed evolution / PaDaI / unspecific peroxygenase / UPO / heme-thiolate peroxidase / Agrocybe aegerita / 1-naphthol / 1-Naphthalenol
Function / homology
Function and homology information


unspecific peroxygenase / hydrogen peroxide catabolic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Chloroperoxidase / Chloroperoxidase-like / Chloroperoxidase / Chloroperoxidase-like superfamily / Peroxidase, family 2 / Heme haloperoxidase family profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-NAPHTHOL / PROTOPORPHYRIN IX CONTAINING FE / METHANOL / PHOSPHATE ION / Aromatic peroxygenase
Similarity search - Component
Biological speciesAgrocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.13 Å
AuthorsRamirez-Escudero, M. / Sanz-Aparicio, J.
CitationJournal: Acs Chem.Biol. / Year: 2018
Title: Structural Insights into the Substrate Promiscuity of a Laboratory-Evolved Peroxygenase.
Authors: Ramirez-Escudero, M. / Molina-Espeja, P. / Gomez de Santos, P. / Hofrichter, M. / Sanz-Aparicio, J. / Alcalde, M.
History
DepositionSep 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,12738
Polymers35,9481
Non-polymers3,17937
Water7,891438
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-48 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.086, 57.799, 60.691
Angle α, β, γ (deg.)90.00, 109.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 6 molecules A

#1: Protein Aromatic peroxygenase / AaP / UNSPECIFIC PEROXYGENASE / UPO


Mass: 35947.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe aegerita (fungus) / Gene: APO1 / Plasmid: pPiczalphaB / Production host: Komagataella phaffii CBS 7435 (fungus) / Strain (production host): X-33 / References: UniProt: B9W4V6, unspecific peroxygenase
#5: 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.: 5
Source method: isolated from a genetically manipulated source
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 , 8 types, 470 molecules

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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-1NP / 1-NAPHTHOL / naphthalen-1-ol


Mass: 144.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O
#9: Chemical...
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH4O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.15 % / Description: Cluster of plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.6M sodium potassium phosphate pH 5.6, 3% MPD, soaking 100mM 1-Naphthol, 20% methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2015 / Details: KB mirrors
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.13→48.04 Å / Num. obs: 124527 / % possible obs: 99 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Net I/σ(I): 13.1
Reflection shellResolution: 1.13→1.14 Å / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2 / Num. unique obs: 5458 / Rpim(I) all: 0.369

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS0.72data reduction
Aimless0.5.32data scaling
MOLREP11.5.02phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5OXU

5oxu


Resolution: 1.13→48.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.454 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17536 6134 4.9 %RANDOM
Rwork0.16596 ---
obs0.16642 118360 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.996 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.45 Å2
2---0.68 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.13→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 206 438 3154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192878
X-RAY DIFFRACTIONr_bond_other_d0.0040.022586
X-RAY DIFFRACTIONr_angle_refined_deg1.3512.0163914
X-RAY DIFFRACTIONr_angle_other_deg0.96135952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4423.63135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91815397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0541521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213267
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02634
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.1271373
X-RAY DIFFRACTIONr_mcbond_other0.5161.1041348
X-RAY DIFFRACTIONr_mcangle_it0.9251.6571702
X-RAY DIFFRACTIONr_mcangle_other0.9241.661703
X-RAY DIFFRACTIONr_scbond_it0.7231.2441505
X-RAY DIFFRACTIONr_scbond_other0.7231.2451506
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1751.8292213
X-RAY DIFFRACTIONr_long_range_B_refined3.9853574
X-RAY DIFFRACTIONr_long_range_B_other3.9853575
X-RAY DIFFRACTIONr_rigid_bond_restr26.588350
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded3.343545
LS refinement shellResolution: 1.125→1.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 394 -
Rwork0.24 7931 -
obs--89.72 %

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