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- PDB-7qyz: Crystal structure of a DyP-type peroxidase 6E10 variant from Pseu... -

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Basic information

Entry
Database: PDB / ID: 7qyz
TitleCrystal structure of a DyP-type peroxidase 6E10 variant from Pseudomonas putida
ComponentsDyp-type peroxidase family protein
KeywordsOXIDOREDUCTASE / DyP / heme / Pseudomonas putida / directed evolution
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / Dyp-type peroxidase, C-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dyp-type peroxidase family protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.452 Å
AuthorsBorges, P.T. / Silva, D. / Martins, L.O. / Frazao, C.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionB-LigZymes H2020-MSCA-RISE 2018European Union
Foundation for Science and Technology (FCT)PTDC/BII-BBF/29564/2017 United Kingdom
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase.
Authors: Borges, P.T. / Silva, D. / Silva, T.F.D. / Brissos, V. / Canellas, M. / Lucas, M.F. / Masgrau, L. / Melo, E.P. / Machuqueiro, M. / Frazao, C. / Martins, L.O.
History
DepositionJan 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,9962
Polymers31,3791
Non-polymers6161
Water181
1
A: Dyp-type peroxidase family protein
hetero molecules

A: Dyp-type peroxidase family protein
hetero molecules

A: Dyp-type peroxidase family protein
hetero molecules

A: Dyp-type peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9838
Polymers125,5174
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area13370 Å2
ΔGint-106 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.721, 108.721, 108.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Dyp-type peroxidase family protein


Mass: 31379.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
Gene: PP_3248 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88HV5
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.075 M sodium bromide, 0.05 M sodium fluoride, 0.1 M HEPES pH 7.8, 22.5 % v/v PEG Smear Broad and 0.075 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→48.622 Å / Num. obs: 14987 / % possible obs: 93.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 65.78 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.028 / Net I/σ(I): 17
Reflection shellResolution: 2.45→2.54 Å / Num. unique obs: 2546 / CC1/2: 0.461 / Rpim(I) all: 0.319

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PpDyP WT

Resolution: 2.452→48.622 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.02 / Stereochemistry target values: LS_WUNIT_K1
Details: THE REFINEMENT CONVERGED TO RWORK AND R-FREE OF 0.222 AND 0.255, RESPECTIVELY. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET.
RfactorNum. reflection% reflection
Rfree0.255 14985 100 %
Rwork0.222 14985 -
obs-14985 93.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.8 Å2 / Biso mean: 80.786 Å2 / Biso min: 42.38 Å2
Refinement stepCycle: final / Resolution: 2.452→48.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 43 1 2217
Biso mean--71.59 74.92 -
Num. residues----282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.452-2.47990.3815460.381546100
2.4799-2.5090.37215170.3721517100
2.509-2.53960.36275270.3627527100
2.5396-2.57180.37055100.3705510100
2.5718-2.60560.35435400.3543540100
2.6056-2.64130.35235100.3523510100
2.6413-2.6790.42033850.420338597
2.679-2.7190.3452280.34522896
2.719-2.76150.33654990.336549999
2.7615-2.80680.3085490.308549100
2.8068-2.85520.31035320.3103532100
2.8552-2.90710.29445170.2944517100
2.9071-2.9630.29775390.2977539100
2.963-3.02350.31015210.3101521100
3.0235-3.08920.30345220.3034522100
3.0892-3.1610.30195300.3019530100
3.161-3.24010.28155300.2815530100
3.2401-3.32770.25735340.2573534100
3.3277-3.42560.24715380.2471538100
3.4256-3.53610.23443240.234432462
3.5361-3.66240.22965080.229650898
3.6624-3.8090.20553740.205537499
3.809-3.98230.21274050.212740575
3.9823-4.19220.1875490.187549100
4.1922-4.45460.17875150.1787515100
4.4546-4.79830.16445420.164454299
4.7983-5.28070.18475350.184753597
5.2807-6.04360.22255390.222553999
6.0436-7.60950.19635460.196354699
7.6095-48.6220.15955740.159557497
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)
10.1539-0.1208-0.10080.08720.13240.1825-0.57290.2274-0.441-0.12540.31070.08810.17980.38580.03391.017-0.28090.40840.41910.11040.739237.60226.9684-5.131
20.4737-0.3988-0.29280.38140.06190.392-0.61330.0555-0.1015-0.55140.7527-0.2605-0.00520.35080.10510.7855-0.35720.04340.65210.07820.358240.269345.1835-15.3521
30.11570.12610.03390.05840.02840.0088-0.45180.1521-0.3854-0.69380.53570.3250.2031-0.17730.06850.9156-0.31350.00470.65440.10210.712136.028338.453-15.3137
40.01470.0082-0.0179-0.0002-0.01340.0097-0.00550.0989-0.13020.1313-0.03370.12480.0485-0.6113-0.00650.9513-0.3199-0.08720.75480.26130.765622.159344.504-16.1502
50.23660.02190.13480.53840.13840.5222-0.4377-0.0245-0.20410.06070.58790.45950.00010.04320.25060.6521-0.09470.05990.55380.23050.63932.813146.1859-1.773
60.1293-0.0862-0.0595-0.0174-0.0341-0.0017-0.31020.04320.071-0.63160.5059-0.1050.16990.37930.00010.7547-0.26490.23150.7157-0.11570.460551.552937.7028-10.9745
70.1663-0.0155-0.1920.07970.03120.0775-0.59040.1784-0.2341-0.14360.0534-0.0977-0.08720.5531-0.09210.7789-0.1950.09640.60620.11570.542745.792442.2604-6.8726
80.0035-0.0091-0.00880.0251-0.00910.004-0.3915-0.4899-0.0755-0.06220.10170.26760.12280.24140.00010.65490.18480.24360.58030.2210.64843.959133.340813.3049
90.0271-0.0256-0.01880.0145-0.00680.0282-0.13790.0582-0.1068-0.0956-0.1332-0.24060.23290.0982-0.00011.2707-0.25230.24580.90630.28641.689531.650324.85335.9647
100.14920.0886-0.05430.1938-0.15860.1451-0.02280.16830.01910.0456-0.010.06210.0926-0.1637-0.05560.9177-0.59740.13060.73030.55341.455224.507228.0256-6.157
110.5760.54710.4751.07490.39191.3879-0.6759-0.2257-0.17150.11330.39170.3738-0.09270.4197-0.40370.69820.23120.30980.74350.31420.565240.283539.697315.3888
120.56530.3234-0.1160.3892-0.0918-0.0283-0.38880.98270.0170.83710.56330.1706-0.0337-0.7884-0.02160.45070.18130.43690.770.53960.79428.359134.281718.771
130.0017-0.00260.01210.0552-0.03360.03210.0148-0.0388-0.0225-0.0296-0.0029-0.1761-0.1404-0.1589-0.10080.9006-0.15090.56130.73870.64431.346522.177333.09886.6465
140.217-0.0919-0.11060.2504-0.09610.0292-0.4887-0.8885-0.24460.14440.366-0.03940.03430.00020.05750.63790.0470.30360.53270.41170.628441.168339.56743.1311
150.3373-0.13070.45720.16870.00120.8062-1.0161-0.130.03460.2458-0.36820.56780.329-0.29-0.25250.53650.03060.27610.74280.47550.973724.026440.64854.7832
160.1816-0.04810.01491.78420.81581.8588-0.27-0.59640.1548-0.02631.00590.4052-0.4932-0.22861.01560.76680.44970.30180.68480.57540.684731.393646.581315.0229
170.4755-0.5758-0.01180.66150.35590.3096-0.3717-0.067-0.1710.13020.49030.36760.5504-0.46940.14220.7239-0.4262-0.00430.52230.30330.67330.338337.4425-13.5836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:13)A4 - 13
2X-RAY DIFFRACTION2(chain A and resid 14:34)A14 - 34
3X-RAY DIFFRACTION3(chain A and resid 35:56)A35 - 56
4X-RAY DIFFRACTION4(chain A and resid 57:63)A57 - 63
5X-RAY DIFFRACTION5(chain A and resid 64:89)A64 - 89
6X-RAY DIFFRACTION6(chain A and resid 90:103)A90 - 103
7X-RAY DIFFRACTION7(chain A and resid 104:123)A104 - 123
8X-RAY DIFFRACTION8(chain A and resid 124:131)A124 - 131
9X-RAY DIFFRACTION9(chain A and resid 132:142)A132 - 142
10X-RAY DIFFRACTION10(chain A and resid 143:151)A143 - 151
11X-RAY DIFFRACTION11(chain A and resid 152:185)A152 - 185
12X-RAY DIFFRACTION12(chain A and resid 186:207)A186 - 207
13X-RAY DIFFRACTION13(chain A and resid 208:212)A208 - 212
14X-RAY DIFFRACTION14(chain A and resid 213:233)A213 - 233
15X-RAY DIFFRACTION15(chain A and resid 234:245)A234 - 245
16X-RAY DIFFRACTION16(chain A and resid 246:263)A246 - 263
17X-RAY DIFFRACTION17(chain A and resid 264:285)A264 - 285

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