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- PDB-1sdq: Structure of reduced-NO adduct of mesopone cytochrome c peroxidase -

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Basic information

Entry
Database: PDB / ID: 1sdq
TitleStructure of reduced-NO adduct of mesopone cytochrome c peroxidase
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Bifunctional catalyst / cytochrome c peroxidase / Trp191 cation radical / 4-mesoporphyrinone / proximal loop
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
FE-(4-MESOPORPHYRINONE)-R-ISOMER / NITRIC OXIDE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsBhaskar, B. / Immoos, C.E. / Sulc, F. / Cohem, M.S. / Farmer, P.J. / Poulos, T.L.
CitationJournal: To be Published
Title: Crystal structures of resting (Fe3+), reduced (Fe2+) and NO-bound states of mesopone cytochrome c peroxidase (MpCcP) (R-isomer)
Authors: Bhaskar, B. / Immoos, C.E. / Sulc, F. / Cohem, M.S. / Farmer, P.J. / Poulos, T.L.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2383
Polymers33,5711
Non-polymers6672
Water9,782543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.884, 75.625, 50.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHelical bundle protein present in mitochondrial intermembrane space; Protein has distinct distal and proxzimal heme domains. Belongs to P212121 space group with one molecule in the asyymetric unit

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Components

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


Mass: 33571.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCP1, CCP, CPO, YKR066C, OBPYC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-FMI / FE-(4-MESOPORPHYRINONE)-R-ISOMER


Mass: 636.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O5
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-methyl-2,4-pentanediol (MPD), 50mM tris-phosphate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 116 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 13, 2002 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 47110 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 24.27 % / Rmerge(I) obs: 0.098 / Rsym value: 0.158 / Net I/σ(I): 42.79
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.85 / Num. unique all: 1450 / Rsym value: 0.322 / % possible all: 62.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S73
Resolution: 1.69→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 2204 -RANDOM
Rwork0.1929 ---
all-47020 --
obs-43845 93.2 %-
Displacement parametersBiso mean: 23.2468 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 47 543 2986
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011796
X-RAY DIFFRACTIONc_angle_d1.56425
X-RAY DIFFRACTIONo_improper_angle_d0.74573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
1.69-1.750.3831690.397329496.72
1.75-1.820.31881980.318239849.08
1.82-1.90.27792020.252441609.48
1.9-20.20841980.204141849.54
2-2.130.21782370.193241999.57
2.13-2.290.21882250.186742719.74
2.29-2.520.23652400.199743459.9
2.52-2.890.22922380.1832442210.08
2.89-3.640.19532370.1741450810.28
3.64-500.1842600.1739461910.53

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