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- PDB-7anv: Mutational and structural analysis of an ancestral D-type dye dec... -

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Basic information

Entry
Database: PDB / ID: 7anv
TitleMutational and structural analysis of an ancestral D-type dye decolorizing peroxidase
Componentsancestral D-type dye decolorizing peroxidase
KeywordsOXIDOREDUCTASE / Dye decolorizing peroxidase / D-type DyP
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE
Function and homology information
Biological speciesGeotrichum candidum (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRozeboom, H.J. / Fraaije, M.W.
CitationJournal: Febs J. / Year: 2021
Title: Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase.
Authors: Zitare, U.A. / Habib, M.H. / Rozeboom, H. / Mascotti, M.L. / Todorovic, S. / Fraaije, M.W.
History
DepositionOct 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ancestral D-type dye decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,73611
Polymers53,3231
Non-polymers1,41310
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-95 kcal/mol
Surface area19260 Å2
Unit cell
Length a, b, c (Å)59.085, 69.107, 114.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ancestral D-type dye decolorizing peroxidase


Mass: 53323.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geotrichum candidum (yeast)

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Non-polymers , 5 types, 408 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2 M Ammonium sulfate, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→59.15 Å / Num. obs: 55396 / % possible obs: 97 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.02 / Rrim(I) all: 0.068 / Net I/σ(I): 18.2 / Num. measured all: 570286 / Scaling rejects: 1012
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.759 / Num. unique obs: 2057 / CC1/2: 0.682 / Rpim(I) all: 0.422 / Rrim(I) all: 0.874 / % possible all: 75.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSK

6fsk


Resolution: 1.65→59.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.669 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 2715 4.9 %RANDOM
Rwork0.1608 ---
obs0.1625 52613 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.62 Å2 / Biso mean: 27.675 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å2-0 Å20 Å2
2---0.89 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 1.65→59.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 86 398 4100
Biso mean--33.16 34.3 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173536
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.6725205
X-RAY DIFFRACTIONr_angle_other_deg1.4311.5988176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85823.35206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17315600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8121522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024428
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02867
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 152 -
Rwork0.267 2991 -
all-3143 -
obs--75.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.745-0.1112-0.27820.34810.29071.64270.0012-0.0790.00390.02950.00030.0271-0.0005-0.082-0.00160.0806-0.0164-0.01140.07230.01240.0068-2.321-2.458-8.275
23.9588-1.41690.59519.76480.984712.30670.2517-0.0738-0.48430.69220.30630.58332.08650.3249-0.55790.62260.0836-0.08960.16830.08650.14329.45-23.595-9.191
30.3718-0.018-0.30930.14750.01221.12870.0485-0.0850.0148-0.0019-0.0055-0.0158-0.03680.1247-0.0430.0755-0.0146-0.01410.0457-0.00040.007310.533-1.596-19
41.25890.3668-0.34181.23450.81351.27450.04890.10130.1112-0.1538-0.04160.0934-0.1058-0.0852-0.00730.13650.0093-0.00580.06990.01420.03098.789-2.383-38.549
50.5522-0.0551-0.36270.22320.04770.9086-0.0316-0.0694-0.03930.00130.0159-0.01190.13050.08110.01570.10070.0052-0.01530.04720.00990.014611.14-11.117-22.831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 142
2X-RAY DIFFRACTION2A143 - 162
3X-RAY DIFFRACTION3A163 - 332
4X-RAY DIFFRACTION4A333 - 383
5X-RAY DIFFRACTION5A384 - 511

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