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- PDB-1sbm: Crystal Structure of Reduced Mesopone cytochrome c peroxidase (R-... -

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Basic information

Entry
Database: PDB / ID: 1sbm
TitleCrystal Structure of Reduced Mesopone cytochrome c peroxidase (R-isomer)
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Bifunctional catalyst / Proximal loop / Trp191 radical / 4-mesoporphyrin / nitrite reductase
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 / 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. / Cohen, M.S. / Farmer, P.J. / Poulos, T.L.
CitationJournal: To be Published
Title: Crystal Structures of Resting (Fe3+), Reduced (Fe2+) and Reduced-NO adduct of Mesopone cytochrome c peroxidase (MpCcP) - R-isomer
Authors: Bhaskar, B. / Immoos, C.E. / Sulc, F. / Cohen, M.S. / Farmer, P.J. / Poulos, T.L.
History
DepositionFeb 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2082
Polymers33,5711
Non-polymers6371
Water10,503583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.826, 75.666, 50.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHelical bundle protein present in intermembrane space of Baker's yeast. Protein is divided into 2 distinct distal and proximal heme domians. Protein belongs to P212121 space group with one molecule in the asymmetric 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 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 59.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-methyl-2,4-pentanediol (MPD), 100mM potassium phosphate, pH 6.0, 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 IV / Detector: IMAGE PLATE / Date: Jun 10, 2003 / 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: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.32 % / Rmerge(I) obs: 0.062 / Rsym value: 0.043 / Net I/σ(I): 20.98
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2236 / Rsym value: 0.534 / % possible all: 96.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1S73
Resolution: 1.69→1.72 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 480 -RANDOM
Rwork0.1812 ---
all-47041 --
obs-46561 99 %-
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.69→1.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 44 583 3021
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005783
X-RAY DIFFRACTIONc_angle_d1.27156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.30107
X-RAY DIFFRACTIONo_improper_angle_d0.77778
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 (%)
1.69-1.750.38452160.42643069.24
1.75-1.820.30832220.297543989.45
1.82-1.90.25322140.224244039.45
1.9-20.19622110.195943989.45
2-2.130.20992470.190143969.44
2.13-2.290.19712330.181343849.42
2.29-2.520.2022500.18344029.45
2.52-2.890.20662370.166144539.56
2.89-3.640.16712340.149744869.63
3.64-500.17652550.153346169.91

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