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- PDB-6fl2: Crystal structure of a dye-decolorizing peroxidase D143A variant ... -

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Basic information

Entry
Database: PDB / ID: 6fl2
TitleCrystal structure of a dye-decolorizing peroxidase D143A 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
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 / NITRITE ION / Peroxidase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27000110594 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 25, 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 1.3Jan 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)68,37710
Polymers66,8192
Non-polymers1,5588
Water14,322795
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-75 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.760, 76.690, 76.140
Angle α, β, γ (deg.)90.000, 107.790, 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

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Protein , 1 types, 2 molecules AB

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


Mass: 33409.594 Da / Num. of mol.: 2 / Mutation: D143A
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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0W8ATM9, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 5 types, 803 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 23% w/v PEG 3350, 0.1 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: 1.27→52.69 Å / Num. all: 346778 / Num. obs: 142004 / % possible obs: 97.21 % / Redundancy: 1.4 % / Biso Wilson estimate: 12.7807580788 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03012 / Rpim(I) all: 0.02269 / Rrim(I) all: 0.03792 / Net I/σ(I): 16.61
Reflection shellResolution: 1.27→1.315 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4241 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 14135 / CC1/2: 0.794 / Rpim(I) all: 0.3181 / Rrim(I) all: 0.5324 / % possible all: 96.98

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Processing

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

6fks


Resolution: 1.27000110594→52.6839422655 Å / SU ML: 0.101396108917 / Cross valid method: FREE R-VALUE / σ(F): 1.34751905903 / Phase error: 12.7920964939
RfactorNum. reflection% reflection
Rfree0.140849286858 6954 4.89756248723 %
Rwork0.114210014854 --
obs0.115502274903 141989 97.2141204179 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.6598735573 Å2
Refinement stepCycle: LAST / Resolution: 1.27000110594→52.6839422655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 106 795 5578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009506168985325003
X-RAY DIFFRACTIONf_angle_d1.075385632476805
X-RAY DIFFRACTIONf_chiral_restr0.0826241502766710
X-RAY DIFFRACTIONf_plane_restr0.00747746439931900
X-RAY DIFFRACTIONf_dihedral_angle_d14.9414596851824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28440.2602381127752130.1990660545344458X-RAY DIFFRACTION96.8685192866
1.2844-1.29950.2222922711882190.1841794702154520X-RAY DIFFRACTION96.7735348172
1.2995-1.31540.2067602744552200.166777334964504X-RAY DIFFRACTION97.3017507724
1.3154-1.3320.2020451022592160.1561111284494493X-RAY DIFFRACTION97.3940020683
1.332-1.34960.199036107712280.1489780239434488X-RAY DIFFRACTION98.127340824
1.3496-1.36810.2039688672582390.1442157885154554X-RAY DIFFRACTION98.1166837257
1.3681-1.38760.1691358888972350.1380270426694491X-RAY DIFFRACTION98.0497925311
1.3876-1.40830.1690040986022210.131523352034582X-RAY DIFFRACTION98.2409490693
1.4083-1.43030.1615086023892260.1241780493294501X-RAY DIFFRACTION98.0298631273
1.4303-1.45380.1518754389972600.1113650602494522X-RAY DIFFRACTION98.1325672071
1.4538-1.47890.1472070304592410.1078381378984499X-RAY DIFFRACTION97.4907445496
1.4789-1.50570.1701331274132230.1062728412074500X-RAY DIFFRACTION97.3011948908
1.5057-1.53470.1402035195742390.1004866549854518X-RAY DIFFRACTION97.7398808301
1.5347-1.5660.1475203354082360.09721134955814477X-RAY DIFFRACTION97.6787564767
1.566-1.60010.1372313074652240.09768827888164524X-RAY DIFFRACTION97.8969072165
1.6001-1.63730.1400162035922420.09017720667194561X-RAY DIFFRACTION97.7809446254
1.6373-1.67830.1306071293652250.08737623650644507X-RAY DIFFRACTION97.8292329957
1.6783-1.72360.1359566533542510.08780027652394492X-RAY DIFFRACTION97.8341584158
1.7236-1.77440.1264240961052350.08889745638564524X-RAY DIFFRACTION97.400736799
1.7744-1.83160.1347891650412510.09146024972664460X-RAY DIFFRACTION97.3347107438
1.8316-1.89710.1382116155922500.0929422110664463X-RAY DIFFRACTION96.7563128721
1.8971-1.97310.1108918539842420.08958570952274454X-RAY DIFFRACTION96.2887020709
1.9731-2.06290.1175369676532130.08814505811134454X-RAY DIFFRACTION95.9695661115
2.0629-2.17160.1150638752522420.09188125857274432X-RAY DIFFRACTION96.09375
2.1716-2.30770.125238456312270.1008467610374523X-RAY DIFFRACTION96.2317666126
2.3077-2.48590.1303914509972240.1085030094924461X-RAY DIFFRACTION96.2803123716
2.4859-2.7360.1461500428272510.1137529259344424X-RAY DIFFRACTION95.6423895254
2.736-3.13190.1436881528922100.1211239379164479X-RAY DIFFRACTION96.0073710074
3.1319-3.94570.1257493515812240.1209118356624573X-RAY DIFFRACTION97.3812423873
3.9457-52.72930.1492878802312270.1456618295214597X-RAY DIFFRACTION96.5572457966

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