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- PDB-6fkt: Crystal structure of a dye-decolorizing peroxidase R232A variant ... -

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Basic information

Entry
Database: PDB / ID: 6fkt
TitleCrystal structure of a dye-decolorizing peroxidase R232A 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: 1.86002782211 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: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_validate_close_contact
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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,9925
Polymers66,7352
Non-polymers1,2573
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-62 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.160, 91.160, 247.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-799-

HOH

21B-670-

HOH

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Components

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


Mass: 33367.488 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: R232A
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


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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298.15 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: 0.996 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: 0.996 Å / Relative weight: 1
ReflectionResolution: 1.86→75.23 Å / Num. obs: 51833 / % possible obs: 99.26 % / Redundancy: 6.4 % / Biso Wilson estimate: 27.2494625903 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1134 / Rpim(I) all: 0.04821 / Rrim(I) all: 0.1235 / Net I/σ(I): 12.11
Reflection shellResolution: 1.86→1.927 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.701 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4908 / CC1/2: 0.589 / Rpim(I) all: 0.7093 / Rrim(I) all: 1.847 / % possible all: 96.57

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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: 1.86002782211→75.2221720275 Å / SU ML: 0.21672739977 / Cross valid method: FREE R-VALUE / σ(F): 1.32698463845 / Phase error: 21.1932223435
RfactorNum. reflection% reflection
Rfree0.207380987407 2566 4.96267357753 %
Rwork0.167661898902 --
obs0.169650100112 51706 99.2590033019 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.6521148601 Å2
Refinement stepCycle: LAST / Resolution: 1.86002782211→75.2221720275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 87 488 5219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004348006066524838
X-RAY DIFFRACTIONf_angle_d0.7311442868286570
X-RAY DIFFRACTIONf_chiral_restr0.0443890317228686
X-RAY DIFFRACTIONf_plane_restr0.00341719768381866
X-RAY DIFFRACTIONf_dihedral_angle_d10.28597208452828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.89580.3126112406761310.2847194944892598X-RAY DIFFRACTION96.7044649185
1.8958-1.93450.355925821451530.3057517832362584X-RAY DIFFRACTION96.7137809187
1.9345-1.97660.273301611261610.237898776942630X-RAY DIFFRACTION98.4479717813
1.9766-2.02260.2456262905741320.2065102067292674X-RAY DIFFRACTION99.0469466996
2.0226-2.07310.22949437881530.1935484236992671X-RAY DIFFRACTION99.4016191482
2.0731-2.12920.2385452111341370.1905822811952689X-RAY DIFFRACTION99.6473906911
2.1292-2.19190.2290731489831320.1856922234992705X-RAY DIFFRACTION99.5787995788
2.1919-2.26260.245071718561370.193802872492686X-RAY DIFFRACTION99.1570073762
2.2626-2.34350.2737385383441350.1677028326482722X-RAY DIFFRACTION99.6859734822
2.3435-2.43730.2204902002971340.1600427236952725X-RAY DIFFRACTION99.8254189944
2.4373-2.54820.24513772521500.1613280595682727X-RAY DIFFRACTION99.8611593197
2.5482-2.68260.2130378882071240.1545146335262767X-RAY DIFFRACTION99.9308676115
2.6826-2.85070.1974443957311370.1601954566092742X-RAY DIFFRACTION99.8959056211
2.8507-3.07080.229569205021370.1633264274162766X-RAY DIFFRACTION99.9311531842
3.0708-3.37980.1868598122061290.1518583631612793X-RAY DIFFRACTION99.7950819672
3.3798-3.86890.1861039390421450.1412523549092800X-RAY DIFFRACTION99.8305084746
3.8689-4.87420.1309614956881780.1230462485642819X-RAY DIFFRACTION99.7005988024
4.8742-75.28370.2305874756011610.1972191261493042X-RAY DIFFRACTION99.3486352357
Refinement TLS params.Method: refined / Origin x: 11.7947656621 Å / Origin y: 23.8383687836 Å / Origin z: 17.3385096472 Å
111213212223313233
T0.194252762533 Å2-0.0136711407432 Å2-0.00761812809618 Å2-0.19405670765 Å20.00857502232979 Å2--0.224451814676 Å2
L0.482984314739 °2-0.112215100593 °20.0248507019714 °2-0.471339590393 °20.138631671053 °2--0.749078174582 °2
S-0.00931848249132 Å °-0.0478778082053 Å °0.00601383859059 Å °0.0277229957389 Å °0.00829962577214 Å °0.0133764700408 Å °0.0719916310651 Å °-0.0851350024505 Å °0.000578681976443 Å °
Refinement TLS groupSelection details: all

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