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- PDB-5oxt: DIRECT-EVOLUTIONED UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA... -

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Basic information

Entry
Database: PDB / ID: 5oxt
TitleDIRECT-EVOLUTIONED UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA, IN COMPLEX WITH ACETATE
ComponentsUNSPECIFIC PEROXYGENASE
KeywordsOXIDOREDUCTASE / directed evolution / PaDaI / unspecific peroxygenase / UPO / heme-thiolate peroxidase / Agrocybe aegerita / acetate
Function / homology
Function and homology information


unspecific peroxygenase / peroxidase activity / hydrogen peroxide catabolic process / 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Aromatic peroxygenase
Similarity search - Component
Biological speciesAgrocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_asym_id / _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_asym_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 1.3Jan 17, 2024Group: Data collection / Database references ...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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNSPECIFIC PEROXYGENASE
B: UNSPECIFIC PEROXYGENASE
C: UNSPECIFIC PEROXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,16232
Polymers107,8443
Non-polymers5,31829
Water23,0951282
1
A: UNSPECIFIC PEROXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,84811
Polymers35,9481
Non-polymers1,90010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UNSPECIFIC PEROXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,68611
Polymers35,9481
Non-polymers1,73810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UNSPECIFIC PEROXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,62710
Polymers35,9481
Non-polymers1,6799
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.999, 99.151, 83.890
Angle α, β, γ (deg.)90.00, 103.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 327 / Label seq-ID: 1 - 327

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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Protein / Sugars , 2 types, 16 molecules ABC

#1: Protein UNSPECIFIC PEROXYGENASE / / UPO


Mass: 35947.934 Da / Num. of mol.: 3 / Mutation: V57A, L67F, V75I, I248V, F311L
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) / Variant (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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
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 , 5 types, 1298 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1282 / 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: 2.45 Å3/Da / Density % sol: 49.91 % / Description: elongated bars
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Sodium acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2014 / Details: KB mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.42→45.23 Å / Num. obs: 190184 / % possible obs: 97.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 19.2
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 6.8 / Num. unique obs: 8694 / CC1/2: 0.972 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS0.72data reduction
Aimless0.5.32data scaling
MOLREP11.5.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YOR

2yor


Resolution: 1.42→45.23 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.721 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16423 9541 5 %RANDOM
Rwork0.15031 ---
obs0.15101 180609 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.29 Å2
2---0.21 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.42→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7590 0 345 1282 9217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198316
X-RAY DIFFRACTIONr_bond_other_d0.0020.027254
X-RAY DIFFRACTIONr_angle_refined_deg1.331211387
X-RAY DIFFRACTIONr_angle_other_deg0.956316856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66651004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23223.697403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.114151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2291561
X-RAY DIFFRACTIONr_chiral_restr0.0770.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219533
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021822
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_it0.5271.0883993
X-RAY DIFFRACTIONr_mcbond_other0.5261.0873990
X-RAY DIFFRACTIONr_mcangle_it0.9141.6275000
X-RAY DIFFRACTIONr_mcangle_other0.9141.6275001
X-RAY DIFFRACTIONr_scbond_it0.7821.2144323
X-RAY DIFFRACTIONr_scbond_other0.7821.2154324
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2781.7886388
X-RAY DIFFRACTIONr_long_range_B_refined3.77414.7249871
X-RAY DIFFRACTIONr_long_range_B_other3.46513.6189471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A226180.05
12B226180.05
21A226340.05
22C226340.05
31B225960.03
32C225960.03
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 634 -
Rwork0.182 12423 -
obs--91.33 %

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