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- PDB-7yzt: Crystal structure of a dye-decolorizing (Dyp) peroxidase from Aci... -

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Basic information

Entry
Database: PDB / ID: 7yzt
TitleCrystal structure of a dye-decolorizing (Dyp) peroxidase from Acinetobacter radioresistens
ComponentsDyp-type peroxidase family protein
KeywordsOXIDOREDUCTASE / biocatalysis / dye-decolorizing / peroxidase / heme
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesAcinetobacter radioresistens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhang, C. / Catucci, G. / Gilardi, G. / Sadeghi, S.J. / Di Nardo, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Crystal structure and functional characterization of a novel bacterial lignin-degrading dye-decolorizing peroxidase.
Authors: Catucci, G. / Zhang, C. / Pernaci, A. / Cappa, F. / Sadeghi, S.J. / Di Nardo, G. / Gilardi, G.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 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 2.0Jan 29, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dyp-type peroxidase family protein
B: Dyp-type peroxidase family protein
C: Dyp-type peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8916
Polymers107,0413
Non-polymers1,8493
Water22,0141222
1
B: Dyp-type peroxidase family protein
C: Dyp-type peroxidase family protein
hetero molecules

A: Dyp-type peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8916
Polymers107,0413
Non-polymers1,8493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2
A: Dyp-type peroxidase family protein
B: Dyp-type peroxidase family protein
C: Dyp-type peroxidase family protein
hetero molecules

A: Dyp-type peroxidase family protein
B: Dyp-type peroxidase family protein
C: Dyp-type peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,78112
Polymers214,0826
Non-polymers3,6996
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area21020 Å2
ΔGint-207 kcal/mol
Surface area69260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.140, 88.140, 231.569
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-755-

HOH

21B-924-

HOH

31B-928-

HOH

41C-779-

HOH

51C-806-

HOH

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Components

#1: Protein Dyp-type peroxidase family protein


Mass: 35680.414 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter radioresistens (bacteria)
Gene: HMPREF0018_02696 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→46.13 Å / Num. obs: 89853 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.23 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.119 / Net I/σ(I): 8.6
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.825 / Num. unique obs: 4559 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GT2

5gt2


Resolution: 1.85→46.13 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.88 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 4507 5.02 %
Rwork0.166 85258 -
obs0.168 89765 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.78 Å2 / Biso mean: 25.98 Å2 / Biso min: 13.54 Å2
Refinement stepCycle: final / Resolution: 1.85→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7287 0 129 1222 8638
Biso mean--22.58 33.12 -
Num. residues----918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.29151750.24327972972100
1.87-1.890.24551270.23328242951100
1.89-1.920.27041560.228428463002100
1.92-1.940.25921180.212127832901100
1.94-1.970.25521710.20528303001100
1.97-1.990.21921300.20172771290199
1.99-2.020.21491460.198127842930100
2.02-2.050.22651600.190828453005100
2.05-2.080.20711350.182127982933100
2.08-2.120.21611560.178928473003100
2.12-2.150.24641320.17528302962100
2.15-2.190.23191580.16927782936100
2.19-2.240.22191840.172727842968100
2.24-2.280.2151470.16428262973100
2.28-2.330.21511390.171528312970100
2.33-2.390.19961370.172228522989100
2.39-2.440.21231390.172328192958100
2.44-2.510.23061500.176928372987100
2.51-2.580.21022040.174427852989100
2.58-2.670.20951230.174628712994100
2.67-2.760.20431370.16928372974100
2.76-2.870.22191450.1728192964100
2.87-30.19641510.170628623013100
3-3.160.21650.171628613026100
3.16-3.360.19591510.162728723023100
3.36-3.620.20071330.14542872300599
3.62-3.980.14131800.131928713051100
3.99-4.560.14071400.12552912305299
4.56-5.740.161530.145429373090100
5.75-46.130.18421650.18583077324299
Refinement TLS params.Method: refined / Origin x: 28.7749 Å / Origin y: 15.9381 Å / Origin z: 4.5745 Å
111213212223313233
T0.109 Å20.0249 Å2-0.0271 Å2-0.1703 Å2-0.0009 Å2--0.1591 Å2
L0.009 °20.0387 °2-0.0568 °2-0.2245 °20.0161 °2--0.2385 °2
S-0.0101 Å °-0.0111 Å °-0.0133 Å °0.0186 Å °0.0328 Å °-0.0094 Å °0.0261 Å °0.014 Å °0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 306
2X-RAY DIFFRACTION1ALLA401 - 923
3X-RAY DIFFRACTION1ALLB1 - 306
4X-RAY DIFFRACTION1ALLB401 - 949
5X-RAY DIFFRACTION1ALLC1 - 306
6X-RAY DIFFRACTION1ALLC401 - 870

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