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- PDB-6fks: Crystal structure of a dye-decolorizing peroxidase from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 6fks
TitleCrystal structure of a dye-decolorizing peroxidase 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 / Peroxidase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.60000463928 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 24, 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 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_seq_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.ref_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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)68,55710
Polymers66,9072
Non-polymers1,6508
Water9,458525
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-79 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.520, 75.850, 75.640
Angle α, β, γ (deg.)90.000, 107.860, 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: 33453.605 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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0W8ATM9, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#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 / References: UniProt: A0A0W8ATM9*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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 / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
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: Diamond / Beamline: I24 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→52.22 Å / Num. obs: 69426 / % possible obs: 96.86 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.7363405784 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04149 / Rpim(I) all: 0.02764 / Rrim(I) all: 0.05004 / Net I/σ(I): 16.64
Reflection shellResolution: 1.6→1.675 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4457 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 6619 / CC1/2: 0.802 / Rpim(I) all: 0.3253 / Rrim(I) all: 0.5549 / % possible all: 93.09

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5de0

5de0


Resolution: 1.60000463928→52.2177435523 Å / SU ML: 0.141380258865 / Cross valid method: FREE R-VALUE / σ(F): 1.34753647333 / Phase error: 16.1468497068
RfactorNum. reflection% reflection
Rfree0.166994977276 3418 4.9253559283 %
Rwork0.128096361396 --
obs0.130008679742 69396 96.8663195656 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.7530478625 Å2
Refinement stepCycle: LAST / Resolution: 1.60000463928→52.2177435523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 112 525 5282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007200049119564908
X-RAY DIFFRACTIONf_angle_d0.9665390272966663
X-RAY DIFFRACTIONf_chiral_restr0.105194691885692
X-RAY DIFFRACTIONf_plane_restr0.00492307382527878
X-RAY DIFFRACTIONf_dihedral_angle_d13.10253017962874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62290.21229102751230.1785494292812523X-RAY DIFFRACTION88.9112903226
1.6229-1.64710.2163641636641510.1790622145762689X-RAY DIFFRACTION95.7195820694
1.6471-1.67280.2617389570931560.163756127762690X-RAY DIFFRACTION96.1811422778
1.6728-1.70030.2332707430721500.1588248777062706X-RAY DIFFRACTION96.4213369345
1.7003-1.72960.225634884351260.1432988859812766X-RAY DIFFRACTION96.6254594053
1.7296-1.7610.2108764190091420.1350789433122736X-RAY DIFFRACTION96.7069892473
1.761-1.79490.1725966942171400.1327423644282721X-RAY DIFFRACTION96.6554054054
1.7949-1.83150.1901609734441170.1277384214782751X-RAY DIFFRACTION96.2416107383
1.8315-1.87140.183084500881290.1228953372272708X-RAY DIFFRACTION95.4897340963
1.8714-1.91490.1873060240891310.1172383179122782X-RAY DIFFRACTION98.578680203
1.9149-1.96280.1487233217171440.1042700313312750X-RAY DIFFRACTION97.3100201748
1.9628-2.01590.1779717048711430.1001546384042791X-RAY DIFFRACTION97.7022977023
2.0159-2.07520.1686277611141630.09944814236252761X-RAY DIFFRACTION98.5175202156
2.0752-2.14220.1623948185921380.1026932858792777X-RAY DIFFRACTION97.8516280631
2.1422-2.21870.1567257271991410.1049913479552747X-RAY DIFFRACTION97.1736204576
2.2187-2.30760.148506084661680.1025329232022735X-RAY DIFFRACTION97.1227835396
2.3076-2.41260.140490490231520.1055806760582790X-RAY DIFFRACTION97.9686979687
2.4126-2.53980.1918455322151130.115472086062809X-RAY DIFFRACTION98.0866062437
2.5398-2.69890.1653985924161530.1162928910272783X-RAY DIFFRACTION98.3255190891
2.6989-2.90730.1586585788931570.1223047626992752X-RAY DIFFRACTION97.3560910308
2.9073-3.19980.1669860004331550.1242887851662769X-RAY DIFFRACTION97.0139349701
3.1998-3.66270.1422404875691480.1244651756212792X-RAY DIFFRACTION98.1308411215
3.6627-4.61420.1375252109721400.1199778198382795X-RAY DIFFRACTION97.217621729
4.6142-52.24550.1892738486511380.1902061048532855X-RAY DIFFRACTION97.4918566775

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