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- PDB-6rpd: Structure of ferrous KpDyP in complex with cyanide -

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Basic information

Entry
Database: PDB / ID: 6rpd
TitleStructure of ferrous KpDyP in complex with cyanide
ComponentsIron-dependent peroxidase
KeywordsOXIDOREDUCTASE / heme protein
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPfanzagl, V. / Beale, J. / Hofbauer, S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: X-ray-induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner.
Authors: Pfanzagl, V. / Beale, J.H. / Michlits, H. / Schmidt, D. / Gabler, T. / Obinger, C. / Djinovic-Carugo, K. / Hofbauer, S.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)68,88515
Polymers66,9072
Non-polymers1,97813
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-82 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.570, 75.740, 75.710
Angle α, β, γ (deg.)90.00, 107.85, 90.00
Int Tables number4
Space group name H-MP1211

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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: 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 (E. coli)
References: UniProt: A0A0W8ATM9, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Non-polymers , 5 types, 573 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / 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: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.06 Å3/Da / Density % sol: 40.37 % / Description: cubic
Crystal growTemperature: 293.15 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.991874 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991874 Å / Relative weight: 1
ReflectionResolution: 1.52→40.62 Å / Num. obs: 81557 / % possible obs: 97.8 % / Redundancy: 3 % / Biso Wilson estimate: 21.31 Å2 / Net I/σ(I): 10.2
Reflection shellResolution: 1.52→1.53 Å / Redundancy: 3.2 % / Num. unique obs: 956 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FKS

6fks


Resolution: 1.52→40.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4058 4.98 %RANDOM
Rwork0.171 ---
obs0.172 81529 97.6 %-
Displacement parametersBiso mean: 25.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.2165 Å20 Å22.3324 Å2
2---1.8187 Å20 Å2
3----0.3978 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.52→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 134 560 5344
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0129890HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217838HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2174SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1655HARMONIC5
X-RAY DIFFRACTIONt_it9890HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion15.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion610SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle10HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11381SEMIHARMONIC4
LS refinement shellResolution: 1.52→1.53 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2575 -5.82 %
Rwork0.2221 1536 -
all0.2241 1631 -
obs--98.34 %
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)
10.36730.00980.06280.3686-0.09730.15730.00920.01520.0386-0.0309-0.01310.00090.03730.00090.004-0.0046-0.0042-0.0031-0.02720.0048-0.007513.75762.9011-2.0851
20.45960.12690.19790.12470.17240.5074-0.0266-0.05430.02130.02310.0078-0.00490.038-0.00010.0188-0.01720.0175-0.00670.0021-0.0084-0.029724.81391.519232.2272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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