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- PDB-1kxn: Crystal Structure of Cytochrome c Peroxidase with a Proposed Elec... -

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Basic information

Entry
Database: PDB / ID: 1kxn
TitleCrystal Structure of Cytochrome c Peroxidase with a Proposed Electron Transfer Pathway Excised to Form a Ligand Binding Channel.
Componentscytochrome c peroxidase
KeywordsOXIDOREDUCTASE / engineered heme channel
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRosenfeld, R.J. / Hayes, A.M.A. / Musah, R.A. / Goodin, D.B.
CitationJournal: Protein Sci. / Year: 2002
Title: Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel.
Authors: Rosenfeld, R.J. / Hays, A.M. / Musah, R.A. / Goodin, D.B.
History
DepositionFeb 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5452
Polymers32,9291
Non-polymers6161
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.800, 75.800, 51.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cytochrome c peroxidase /


Mass: 32928.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-362, NUMBERED 4-292 / Mutation: P190G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCP-MKT / Plasmid: PT7CCP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 15 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.06 mMprotein1drop
280-120 mMpotassium phosphate1droppH6.0
320 %MPD1drop
425 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 35095 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.075
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Num. unique all: 3208 / % possible all: 81.1
Reflection
*PLUS
Num. obs: 36741 / Num. measured all: 168657 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 81.1 % / Num. unique obs: 3208 / Num. measured obs: 11517 / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
XFITdata reduction
SHELXLrefinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMQ
Resolution: 1.8→10 Å / Num. parameters: 10827 / Num. restraintsaints: 9732 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 --random
Rwork0.187 ---
all-35095 --
obs-35095 46.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2706
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 43 348 2706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.029
X-RAY DIFFRACTIONc_bond_d0.009
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.1871
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.2 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d

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