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- PDB-1s73: Crystal Structure of Mesopone Cytochrome c Peroxidase (R-isomer) ... -

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Basic information

Entry
Database: PDB / ID: 1s73
TitleCrystal Structure of Mesopone Cytochrome c Peroxidase (R-isomer) [MpCcP-R]
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Bifunctional catalyst / proximal loop / Trp191 radical / mesoporphyrin / nitrite reductase / cyctochrome c peroxidase / cytochorme oxidase
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
FE-(4-MESOPORPHYRINONE)-R-ISOMER / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBhaskar, B. / Immoos, C.E. / Sulc, F. / Choen, M.S. / Farmer, P.J. / Poulos, T.L.
CitationJournal: To be Published
Title: Crystal structures of reduced, resting and NO-bound states of mesopone cytochorme c peroxidase (MpCcP) (R-isomer)
Authors: Bhaskar, B. / Immoos, C.E. / Sulc, F. / Choen, M.S. / Farmer, P.J. / Poulos, T.L.
History
DepositionJan 28, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2082
Polymers33,5711
Non-polymers6371
Water12,719706
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.980, 76.149, 51.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHelical bundle protein with a distinct distal and proximal domains separated by heme. Proximal heme domain also comntains the loop comprising residues (189-195) which form the loop. Trp191 of this proximal loop forms the radical during catalysis and electron transfer.

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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.: 706 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: tris-phosphate buffer, 2-methyl-2,4-pentanediol, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 11, 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: 1.53→50 Å / Num. obs: 62259 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Rmerge(I) obs: 0.05 / Rsym value: 0.052 / Net I/σ(I): 50
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 5.83 / Num. unique all: 2337 / Rsym value: 0.146 / % possible all: 73.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WTCCP - ultra-high resolution structure

Resolution: 1.53→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
Rfree0.2016 3095 -RANDOM
Rwork0.1829 ---
all-63802 --
obs-62085 97.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.2016 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 44 706 3139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005543
X-RAY DIFFRACTIONc_angle_d2.38645
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 (%)
1.53-1.580.39082450.384647757.69
1.58-1.650.28793020.275457489.25
1.65-1.720.22553210.217459719.61
1.72-1.810.22422850.199160289.7
1.81-1.930.20912980.190160249.7
1.93-2.080.2023280.1960249.7
2.08-2.290.19883120.184460439.73
2.29-2.620.20123420.183360629.7
2.62-3.30.18833160.162461309.87
3.3-500.17893460.156761859.96

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