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- PDB-7o9l: Dictyostelium discoideum dye decolorizing peroxidase DyPA in comp... -

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Basic information

Entry
Database: PDB / ID: 7o9l
TitleDictyostelium discoideum dye decolorizing peroxidase DyPA in complex with cyanide.
ComponentsDyPA
KeywordsHYDROLASE / Dye decolorizing-type peroxidase / Dictyostelium discoideum / B-type DyP
Function / homology
Function and homology information


peroxidase activity / protein dimerization activity / heme binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRai, A. / Fedorov, R. / Manstein, D.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2155 - 39087428-B11 Germany
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum .
Authors: Rai, A. / Klare, J.P. / Reinke, P.Y.A. / Englmaier, F. / Fohrer, J. / Fedorov, R. / Taft, M.H. / Chizhov, I. / Curth, U. / Plettenburg, O. / Manstein, D.J.
History
DepositionApr 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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: DyPA
B: DyPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,57213
Polymers70,8532
Non-polymers1,71911
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-35 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.050, 141.050, 95.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein DyPA


Mass: 35426.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB0168077, DDB0217308 / Production host: Escherichia coli (E. coli) / References: UniProt: Q556V8
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 2.4 M Sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91985 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91985 Å / Relative weight: 1
ReflectionResolution: 1.85→47.74 Å / Num. obs: 82374 / % possible obs: 100 % / Redundancy: 26.4 % / Biso Wilson estimate: 25.87 Å2 / Rmerge(I) obs: 0.0394 / Net I/σ(I): 15.36
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 26.22 % / Rmerge(I) obs: 0.36 / Num. unique obs: 10792 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O9J

7o9j


Resolution: 1.85→45.22 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1799 4123 5.01 %
Rwork0.1546 78169 -
obs0.1559 82292 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.08 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 118 393 5429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075135
X-RAY DIFFRACTIONf_angle_d1.10266926
X-RAY DIFFRACTIONf_chiral_restr0.0773744
X-RAY DIFFRACTIONf_plane_restr0.005886
X-RAY DIFFRACTIONf_dihedral_angle_d12.1052711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.30171340.2682681X-RAY DIFFRACTION99.96
1.87-1.890.2441260.23982661X-RAY DIFFRACTION99.96
1.89-1.920.26391320.22392668X-RAY DIFFRACTION99.96
1.92-1.940.22681380.20392648X-RAY DIFFRACTION100
1.94-1.970.21411340.1822669X-RAY DIFFRACTION100
1.97-20.21841300.17212681X-RAY DIFFRACTION99.96
2-2.030.19031430.15912677X-RAY DIFFRACTION100
2.03-2.060.1481350.16132639X-RAY DIFFRACTION100
2.06-2.090.18181390.15652661X-RAY DIFFRACTION100
2.09-2.130.21081400.15172681X-RAY DIFFRACTION100
2.13-2.170.18891370.14432677X-RAY DIFFRACTION100
2.17-2.210.18411410.15262672X-RAY DIFFRACTION100
2.21-2.260.18741280.14922661X-RAY DIFFRACTION100
2.26-2.30.17831570.14962682X-RAY DIFFRACTION100
2.3-2.360.19661150.14542678X-RAY DIFFRACTION100
2.36-2.420.18941600.14952642X-RAY DIFFRACTION100
2.42-2.480.18231530.1542690X-RAY DIFFRACTION100
2.48-2.560.19231390.1592683X-RAY DIFFRACTION100
2.56-2.640.1961680.15472681X-RAY DIFFRACTION100
2.64-2.730.18741410.15252696X-RAY DIFFRACTION100
2.73-2.840.19841390.15912687X-RAY DIFFRACTION100
2.84-2.970.20061460.14732696X-RAY DIFFRACTION100
2.97-3.130.1961580.15482692X-RAY DIFFRACTION100
3.13-3.320.16691350.14932724X-RAY DIFFRACTION100
3.32-3.580.14771450.13692723X-RAY DIFFRACTION100
3.58-3.940.14861500.13352740X-RAY DIFFRACTION100
3.94-4.510.14711570.12962752X-RAY DIFFRACTION100
4.51-5.680.13651440.14642795X-RAY DIFFRACTION100
5.68-45.220.23121590.18762932X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 9.07372623191 Å / Origin y: 26.3872388582 Å / Origin z: 13.8894603174 Å
111213212223313233
T0.182983943672 Å20.000127154021361 Å20.0115782255618 Å2-0.163041026471 Å2-0.00265672933352 Å2--0.155973560617 Å2
L0.731010940556 °20.0356503521698 °20.191328614111 °2-0.399493735993 °2-0.0937732193032 °2--0.368476040866 °2
S0.0253977977697 Å °-0.0343060747996 Å °0.0184710285122 Å °0.0208194255957 Å °0.00183337730152 Å °0.0216513855796 Å °-0.0323598516211 Å °-0.00616214614121 Å °8.76512148177E-6 Å °
Refinement TLS groupSelection details: all

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