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- PDB-6rr4: Structure of 25% reduced KpDyP -

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Basic information

Entry
Database: PDB / ID: 6rr4
TitleStructure of 25% reduced KpDyP
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
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 17, 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)68,92614
Polymers66,9072
Non-polymers2,01812
Water11,800655
1
A: Iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5558
Polymers33,4541
Non-polymers1,1017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron-dependent peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3716
Polymers33,4541
Non-polymers9175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.889, 76.647, 76.579
Angle α, β, γ (deg.)90.00, 108.01, 90.00
Int Tables number4
Space group name H-MP1211

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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 (E. coli)
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / 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.: 655 / 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: 42.06 %
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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→48.5 Å / Num. obs: 43564 / % possible obs: 98.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 11.68 Å2 / Net I/σ(I): 6.2
Reflection shellResolution: 1.9→1.91 Å / Num. unique obs: 2794

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
X-GENdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FKS

6fks


Resolution: 1.9→48.4 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.811 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.181 982 2.26 %RANDOM
Rwork0.169 ---
obs0.169 43525 98.5 %-
Displacement parametersBiso mean: 12.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.6324 Å20 Å21.2913 Å2
2---2.9278 Å20 Å2
3---0.2954 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.9→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 136 655 5453
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.02410127HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.5918278HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2200SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1689HARMONIC5
X-RAY DIFFRACTIONt_it10127HARMONIC20
X-RAY DIFFRACTIONt_nbd11SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.37
X-RAY DIFFRACTIONt_other_torsion16.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion613SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11518SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.91 Å / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.2505 -2.14 %
Rwork0.2351 870 -
all0.2354 889 -
obs--98.18 %
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)
10.37020.3251-0.07650.0714-0.0719-0.08890.01210.0150.0426-0.0066-0.00460.02560.0279-0.001-0.0075-0.0223-0.0006-0.0012-0.04080.0072-0.028814.20192.0054-2.1586
20.06430.2075-0.019500.0393-0.0195-0.02260.01680.0144-0.01510.0092-0.00730.0107-0.00630.0134-0.03450.0116-0.0052-0.013-0.0046-0.040424.74490.401332.7265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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