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

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Basic information

Entry
Database: PDB / ID: 7odz
TitleDictyostelium discoideum dye decolorizing peroxidase DyPA in complex with an activated form of oxygen and veratryl alcohol
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 / cytosol / cytoplasm
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
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Veratryl alcohol / Dyp-type peroxidase family protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: DyPA
B: DyPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,00913
Polymers70,8532
Non-polymers2,15611
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-43 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.440, 140.440, 95.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 629 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-VOH / Veratryl alcohol / Veratrole alcohol


Mass: 168.190 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.32 Å3/Da / Density % sol: 62.9 %
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: ID23-1 / Wavelength: 0.910003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2014
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.910003 Å / Relative weight: 1
ReflectionResolution: 1.6→47.64 Å / Num. obs: 125165 / % possible obs: 100 % / Redundancy: 33.26 % / Biso Wilson estimate: 21.13 Å2 / Rmerge(I) obs: 0.0224 / Net I/σ(I): 25.13
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 33.48 % / Rmerge(I) obs: 0.2786 / Num. unique obs: 20558 / % possible all: 100

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Processing

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

7o9j


Resolution: 1.6→45.11 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1682 6292 5.03 %
Rwork0.1508 118785 -
obs0.1517 125077 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.24 Å2 / Biso mean: 29.6036 Å2 / Biso min: 13.78 Å2
Refinement stepCycle: final / Resolution: 1.6→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 146 622 5698
Biso mean--29.9 43.49 -
Num. residues----614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.620.25072150.218339004115
1.62-1.640.21712090.198338734082
1.64-1.660.20152000.188639454145
1.66-1.680.19952160.185738974113
1.68-1.70.21341930.183239484141
1.7-1.720.20322270.174438624089
1.72-1.750.1951870.17239424129
1.75-1.770.19582190.174139134132
1.77-1.80.18451910.163939444135
1.8-1.830.17822090.163639084117
1.83-1.860.16712190.156539314150
1.86-1.90.17721980.149339224120
1.9-1.930.15921980.155639434141
1.93-1.970.16212210.148739274148
1.97-2.020.16912070.145739134120
2.02-2.060.17682110.14839374148
2.06-2.110.18212140.147639474161
2.11-2.170.15891940.1439624156
2.17-2.240.16442030.140339514154
2.24-2.310.16262000.142639534153
2.31-2.390.16292190.148539724191
2.39-2.490.18452350.156939114146
2.49-2.60.16142070.157539784185
2.6-2.740.16992260.16139664192
2.74-2.910.19641890.157840024191
2.91-3.130.16182020.159440104212
3.13-3.450.17082120.145140284240
3.45-3.950.14982240.127640344258
3.95-4.970.14382140.127140914305
4.97-45.110.1692330.168542754508
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)
11.2955-0.54850.03414.4460.19822.08530.0380.19280.3906-0.1707-0.06790.1977-0.2444-0.1460.02670.11780.01310.00750.14740.04690.26252.37738.1731.479
24.9889-3.1231-1.4712.09341.44272.62180.17640.34470.6759-0.2171-0.1328-0.4276-0.34910.0043-0.08230.2682-0.03290.01720.24770.10290.322411.47745.328-1.927
31.46540.02290.09170.7665-0.14740.562-0.00810.03770.192-0.01040.0210.0398-0.0831-0.0451-0.01610.18680.01080.00280.16210.01110.17220.03534.9644.419
43.6338-1.27480.90571.421-1.9933.15470.010.5411-0.0776-0.850.00050.05150.1498-0.1291-0.01210.3201-0.0034-0.00280.3470.05420.2089-5.70932.904-13.279
51.69030.8602-0.12793.6336-0.96261.28150.1031-0.1757-0.16790.2663-0.02070.1470.1183-0.0766-0.07040.15680.01450.00060.20130.04030.1793-10.24819.34611.774
64.1991-1.4935-2.52076.33521.62713.51390.03670.2879-0.3532-0.2194-0.05130.43740.1533-0.3162-0.01350.1956-0.026-0.05710.20960.02070.233-16.00212.2622.057
74.70761.60410.21983.38650.9794.1112-0.13170.6402-0.1101-0.53660.0820.5345-0.1265-0.43370.05160.27140.0313-0.06790.27630.01730.26-14.12325.185-5.919
81.919-0.17490.0811.3369-0.47541.01130.03990.09830.1009-0.03030.05890.1795-0.0849-0.102-0.10950.15870.02380.00450.15170.01690.1688-9.69330.5454.978
92.23340.1195-1.2962.5798-1.09434.3455-0.006-0.3157-0.17150.29130.0277-0.05080.24140.06420.04030.1813-0.036-0.04950.16720.02290.126616.27113.43225.619
103.78650.3058-3.26422.3459-1.29148.4165-0.1581-0.2268-0.45710.1086-0.03380.04170.5979-0.22320.25840.2632-0.0242-0.0220.20950.05840.324610.8493.10223.306
111.07570.30590.14831.2146-0.00960.93090.05-0.2188-0.07690.1799-0.0266-0.0226-0.0004-0.0186-0.01470.157-0.0051-0.00830.19360.01820.142217.09618.45924.986
121.28690.1034-0.0843.4439-0.80641.05160.0091-0.0955-0.00080.0297-0.048-0.2181-0.01270.13210.04680.1661-0.0177-0.04150.2157-0.02070.130727.77626.6323.68
133.72570.9383-0.3812.70910.4274.92260.0462-0.07760.07590.13250.0275-0.3674-0.05880.3422-0.04930.185-0.0361-0.03130.1866-0.03130.260937.2237.44220.407
145.63920.4663-0.04334.38850.87613.9534-0.0032-0.2157-0.12830.37320.0565-0.83480.11680.8393-0.06580.23670.0086-0.06030.31330.0190.290436.59123.16926.565
151.30840.07550.29741.7182-0.11941.3718-0.002-0.20860.04390.31010.0017-0.1473-0.16730.13970.00880.2128-0.0329-0.01390.2098-0.01650.152524.86730.83628.664
164.37180.44230.129.93792.18723.77650.0672-0.2237-0.59460.1953-0.0099-0.26890.4530.0361-0.04940.2551-0.0103-0.0410.26080.07830.21521.3817.48330.317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:27 )A0 - 27
2X-RAY DIFFRACTION2( CHAIN A AND RESID 28:51 )A28 - 51
3X-RAY DIFFRACTION3( CHAIN A AND RESID 52:155 )A52 - 155
4X-RAY DIFFRACTION4( CHAIN A AND RESID 156:175 )A156 - 175
5X-RAY DIFFRACTION5( CHAIN A AND RESID 176:202 )A176 - 202
6X-RAY DIFFRACTION6( CHAIN A AND RESID 203:226 )A203 - 226
7X-RAY DIFFRACTION7( CHAIN A AND RESID 227:241 )A227 - 241
8X-RAY DIFFRACTION8( CHAIN A AND RESID 242:306 )A242 - 306
9X-RAY DIFFRACTION9( CHAIN B AND RESID 0:27 )B0 - 27
10X-RAY DIFFRACTION10( CHAIN B AND RESID 28:51 )B28 - 51
11X-RAY DIFFRACTION11( CHAIN B AND RESID 52:155 )B52 - 155
12X-RAY DIFFRACTION12( CHAIN B AND RESID 156:202 )B156 - 202
13X-RAY DIFFRACTION13( CHAIN B AND RESID 203:226 )B203 - 226
14X-RAY DIFFRACTION14( CHAIN B AND RESID 227:241 )B227 - 241
15X-RAY DIFFRACTION15( CHAIN B AND RESID 242:292 )B242 - 292
16X-RAY DIFFRACTION16( CHAIN B AND RESID 293:306 )B293 - 306

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