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- PDB-6h08: The crystal structure of engineered cytochrome c peroxidase from ... -

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Basic information

Entry
Database: PDB / ID: 6h08
TitleThe crystal structure of engineered cytochrome c peroxidase from Saccharomyces cerevisiae with a His175Me-His proximal ligand substitution
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Engineered cytochrome c peroxidase / Saccharomyces cerevisiae / Me-His / proximal ligand
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / 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 / SYNCHROTRON / Resolution: 1.9 Å
AuthorsOrtmayer, M. / Levy, C. / Green, A.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council757991 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M027023/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/ K014706/2, EP/K014668/1, EP/K014854/1, EP/K014714/1, and EP/M013219/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code.
Authors: Ortmayer, M. / Fisher, K. / Basran, J. / Wolde-Michael, E.M. / Heyes, D.J. / Levy, C. / Lovelock, S.L. / Anderson, J.L.R. / Raven, E.L. / Hay, S. / Rigby, S.E.J. / Green, A.P.
History
DepositionJul 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,64515
Polymers102,3413
Non-polymers2,30412
Water13,097727
1
A: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8675
Polymers34,1141
Non-polymers7534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8715
Polymers34,1141
Non-polymers7574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9075
Polymers34,1141
Non-polymers7934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.920, 106.770, 163.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 293
2010B0 - 293
1020A0 - 293
2020C0 - 293
1030B-2 - 294
2030C-2 - 294

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 34113.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00431, cytochrome-c peroxidase

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Non-polymers , 5 types, 739 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5 mM cobalt(II) chloride hexahydrate, 5 mM cadmium chloride hemi(pentahydrate), 5 mM magnesium chloride hexahydrate, 5 mM nickel(II) chloride hexahydrate, 0.1 M HEPES pH 7.5 and 12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.9→81.86 Å / Num. obs: 100412 / % possible obs: 99.11 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/av σ(I): 19.2 / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 4877 / CC1/2: 0.966 / Rpim(I) all: 0.163 / Rrim(I) all: 0.425 / % possible all: 97.15

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.9→81.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.067 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.117
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 4974 5 %RANDOM
Rwork0.1783 ---
obs0.1796 95376 99.05 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 115.81 Å2 / Biso mean: 33.345 Å2 / Biso min: 12.82 Å2
Baniso -1Baniso -2Baniso -3
1-4.54 Å20 Å20 Å2
2---3.44 Å20 Å2
3----1.1 Å2
Refinement stepCycle: final / Resolution: 1.9→81.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7222 0 138 727 8087
Biso mean--26.32 37.75 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197686
X-RAY DIFFRACTIONr_bond_other_d0.0020.026659
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.96510476
X-RAY DIFFRACTIONr_angle_other_deg0.919315535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74324.793411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.266151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7081533
X-RAY DIFFRACTIONr_chiral_restr0.0750.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218765
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021679
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A211400.05
12B211400.05
21A210820.06
22C210820.06
31B214600.06
32C214600.06
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 357 -
Rwork0.264 6881 -
all-7238 -
obs--97.43 %

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