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- PDB-4jb4: Expression, Purification, Characterization, and Solution NMR Stud... -

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Basic information

Entry
Database: PDB / ID: 4jb4
TitleExpression, Purification, Characterization, and Solution NMR Study of Highly Deuterated Yeast Cytochrome c Peroxidase with Enhanced Solubility
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Cytochrome c Peroxidase
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
FLUORIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsWohlkonig, A.C.
CitationJournal: Biochemistry / Year: 2013
Title: Expression, purification, characterization, and solution nuclear magnetic resonance study of highly deuterated yeast cytochrome C peroxidase with enhanced solubility.
Authors: Volkov, A.N. / Wohlkonig, A. / Soror, S.H. / van Nuland, N.A.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
C: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1966
Polymers68,9252
Non-polymers1,2714
Water64936
1
A: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0983
Polymers34,4621
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0983
Polymers34,4621
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.052, 87.920, 87.526
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial / / CCP


Mass: 34462.270 Da / Num. of mol.: 2 / Fragment: cytochrome-c peroxidase, UNP residues 68-361 / Mutation: T1M, T2K, P3T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase
#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
#3: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M NH4Cl, 0.1 M CH3COONa pH5.0 and 20% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 91760 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.158
Reflection shellResolution: 2.39→2.45 Å / % possible all: 90.17

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Processing

Software
NameVersionClassification
HKL-3000data collection
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZBY
Resolution: 2.39→43.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.926 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.502 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27937 1310 5.1 %RANDOM
Rwork0.21214 ---
obs0.2156 24481 98.44 %-
all-24868 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.992 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.39→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 88 36 4828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224938
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9996718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36624.961258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62315794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6771520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213916
X-RAY DIFFRACTIONr_mcbond_it0.7771.52892
X-RAY DIFFRACTIONr_mcangle_it1.46324640
X-RAY DIFFRACTIONr_scbond_it2.39632046
X-RAY DIFFRACTIONr_scangle_it3.6924.52078
LS refinement shellResolution: 2.39→2.44 Å / Num. reflection Rfree: 79 / Num. reflection Rwork: 1655 / Num. reflection obs: 1655 / Total num. of bins used: 20

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