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- PDB-6fiy: Crystal structure of a dye-decolorizing peroxidase D143AR232A var... -

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Basic information

Entry
Database: PDB / ID: 6fiy
TitleCrystal structure of a dye-decolorizing peroxidase D143AR232A variant from Klebsiella pneumoniae (KpDyP)
ComponentsIron-dependent peroxidase
KeywordsOXIDOREDUCTASE / alpha-beta barrel / heme binding / DyP / enzymatic redox reaction
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09000433235 Å
AuthorsPfanzagl, V. / Hofbauer, S. / Mlynek, G.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundW1224 Austria
Austrian Science FundG005416N Austria
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage.
Authors: Pfanzagl, V. / Nys, K. / Bellei, M. / Michlits, H. / Mlynek, G. / Battistuzzi, G. / Djinovic-Carugo, K. / Van Doorslaer, S. / Furtmuller, P.G. / Hofbauer, S. / Obinger, C.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 6, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-dependent peroxidase
B: Iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,29710
Polymers66,6472
Non-polymers1,6508
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-85 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.620, 76.310, 75.940
Angle α, β, γ (deg.)90.000, 107.920, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Iron-dependent peroxidase / Peroxidase / Putative deferrochelatase/peroxidase YfeX


Mass: 33323.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: yfeX, AGG09_21550, B1727_13990, B8011_07420, BL102_0001560, BN49_3985, BVX91_12125, CEO55_07245, CIT28_09840, CP905_14695, PMK1_00271, SAMEA3531778_01640, SM57_03027
Variant: D143AR232A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0W8ATM9, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 29% w/v PEG 3350, 0.15 M MgCl2, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.09→52.47 Å / Num. obs: 224631 / % possible obs: 98.45 % / Redundancy: 2.9 % / Biso Wilson estimate: 11.1684331273 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04589 / Rpim(I) all: 0.0309 / Rrim(I) all: 0.05555 / Net I/σ(I): 10.82
Reflection shellResolution: 1.09→1.129 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 22440 / CC1/2: 0.574 / Rpim(I) all: 0.4891 / Rrim(I) all: 0.8511 / % possible all: 98.58

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FKS

6fks


Resolution: 1.09000433235→52.467343562 Å / SU ML: 0.100314847531 / Cross valid method: FREE R-VALUE / σ(F): 1.34352684958 / Phase error: 14.8246526448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.149571192165 11226 4.99826356423 %Random selection
Rwork0.124624616817 213372 --
obs0.125848428175 224598 98.4556441538 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.1536855966 Å2
Refinement stepCycle: LAST / Resolution: 1.09000433235→52.467343562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 112 777 5554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009638324721035170
X-RAY DIFFRACTIONf_angle_d1.113101779497054
X-RAY DIFFRACTIONf_chiral_restr0.0848591615366736
X-RAY DIFFRACTIONf_plane_restr0.00776087093821940
X-RAY DIFFRACTIONf_dihedral_angle_d14.64839843131895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10240.3109592524613570.2724550840837161X-RAY DIFFRACTION98.6743667148
1.1024-1.11540.2822690985463890.2535457188157021X-RAY DIFFRACTION98.4325185972
1.1154-1.1290.2393115859713890.2357377982487117X-RAY DIFFRACTION98.6333771353
1.129-1.14330.2471880646933600.2255628748747072X-RAY DIFFRACTION98.3459044594
1.1433-1.15830.2333956462443760.2203022863497034X-RAY DIFFRACTION97.9769932566
1.1583-1.17420.2450922311814010.2120823369157045X-RAY DIFFRACTION97.7293608085
1.1742-1.19090.2260640160233650.2041410403926996X-RAY DIFFRACTION97.2262580901
1.1909-1.20870.2351575987563330.1921504732556901X-RAY DIFFRACTION95.0966215328
1.2087-1.22760.210002463673180.1797897628316945X-RAY DIFFRACTION96.4285714286
1.2276-1.24770.1916891698363500.1686895125487240X-RAY DIFFRACTION99.2546096508
1.2477-1.26930.1963550440633840.1639460597737147X-RAY DIFFRACTION99.4848084544
1.2693-1.29230.1875022227053930.1554653585497105X-RAY DIFFRACTION99.5618111805
1.2923-1.31720.1692270165563950.1478025790747134X-RAY DIFFRACTION99.5372818614
1.3172-1.34410.168449692063990.1418134459987215X-RAY DIFFRACTION99.7510808332
1.3441-1.37330.1786578847383870.1379305702517192X-RAY DIFFRACTION99.7630643675
1.3733-1.40530.1641664214373890.1253673834547224X-RAY DIFFRACTION99.8295305534
1.4053-1.44040.1543310900754100.1132648986747138X-RAY DIFFRACTION99.6698798363
1.4404-1.47940.1367612704163420.1044690313267170X-RAY DIFFRACTION99.3519375744
1.4794-1.52290.14113343163570.1019173515167207X-RAY DIFFRACTION99.3172268908
1.5229-1.5720.1371328209633390.09399217854887039X-RAY DIFFRACTION97.2581070393
1.572-1.62820.1332222450733610.09201087073796864X-RAY DIFFRACTION94.8162729659
1.6282-1.69340.1219943104063990.09435365646487196X-RAY DIFFRACTION99.593495935
1.6934-1.77050.1305128551863630.09378783403197183X-RAY DIFFRACTION99.564586357
1.7705-1.86390.1189875729293840.08824578770277186X-RAY DIFFRACTION99.343832021
1.8639-1.98060.1181373759524070.09210320620997134X-RAY DIFFRACTION99.0542493104
1.9806-2.13360.1153134907693610.09453534799827131X-RAY DIFFRACTION98.4494086728
2.1336-2.34830.1144413821994010.0975480979957089X-RAY DIFFRACTION98.0366492147
2.3483-2.68810.1274227685114000.1083144612797098X-RAY DIFFRACTION97.8085050874
2.6881-3.38660.1402691980533500.1235405374697132X-RAY DIFFRACTION97.5743348983
3.3866-52.52820.1551262725793670.1345576692057256X-RAY DIFFRACTION98.1586402266

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