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- PDB-1kok: Crystal Structure of Mesopone Cytochrome c Peroxidase (MpCcP) -

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Basic information

Entry
Database: PDB / ID: 1kok
TitleCrystal Structure of Mesopone Cytochrome c Peroxidase (MpCcP)
ComponentsCytochrome c Peroxidase
KeywordsOXIDOREDUCTASE / Bifunctional catalyst / Proximal loop / Trp191 cationic radical / mesoporphyrin / nitrite reducatse / cytochrome c peroxidase / cytochrome 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(III)-(4-MESOPORPHYRINONE) / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBhaskar, B. / Immoos, C.E. / Cohen, M.S. / Barrows, T.P. / Farmer, P.J. / Poulos, T.L.
CitationJournal: J.Inorg.Biochem. / Year: 2002
Title: Mesopone cytochrome c peroxidase: functional model of heme oxygenated oxidases.
Authors: Immoos, C.E. / Bhaskar, B. / Cohen, M.S. / Barrows, T.P. / Farmer, P.J. / Poulos, T.L.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / pdbx_validate_chiral / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2082
Polymers33,5711
Non-polymers6371
Water11,169620
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.011, 76.091, 51.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHelical bundle protein containing a distinct distal and proximal heme domains. Proximal heme domain contains the loop (190-195) which forms the conduit for electron in the electron transfer with the redox partner Cytochrome c.

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Components

#1: Protein Cytochrome c Peroxidase


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: OPBYC / Plasmid: pT7CcP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HIF / FE(III)-(4-MESOPORPHYRINONE) / FE-MESOPONE / (8,12-DIETHYL-3,8,13,17-TETRAMETHYL-7-OXO-PORPHYRINATO-2,18-DIPROPIONIC ACID)IRON(III)


Mass: 636.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 60.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-Methyl-2,4-Pentanediol, potassium phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown
Details: Sundaramoorthy, M., (1991) J.Am.Chem.Soc., 113, 7755.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
20.05 Mpotassium phosphate12pH6.0
325 %MPD12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 2000 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 46346 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.142 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 37.41
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.41 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 4.9756 / Num. unique all: 2045 / Rsym value: 0.189 / % possible all: 90.1
Reflection
*PLUS
% possible obs: 99.1 % / Num. measured all: 423704 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 90.1 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 4.97

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild Type Cytochrome c Peroxdiase - Ultra-high resolution structure

Resolution: 1.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2269 -RANDOM
Rwork0.1859 ---
all-45673 --
obs-43404 97.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.03 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 44 620 3038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0076
X-RAY DIFFRACTIONc_angle_d1.2576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.7-1.760.32021840.3505X-RAY DIFFRACTION383210
1.76-1.830.26862040.2653X-RAY DIFFRACTION424410
1.83-1.910.23142110.2022X-RAY DIFFRACTION428310
1.91-2.020.18762110.1751X-RAY DIFFRACTION435410
2.02-2.140.20712520.1707X-RAY DIFFRACTION435210
2.14-2.310.19492370.1699X-RAY DIFFRACTION439710
2.31-2.540.20932420.1808X-RAY DIFFRACTION439510
2.54-2.910.21792320.1701X-RAY DIFFRACTION442410
2.91-3.660.20182400.1788X-RAY DIFFRACTION450210
3.66-500.18882560.1811X-RAY DIFFRACTION462110
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.2072 / Rfactor Rwork: 0.1859
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.2576
LS refinement shell
*PLUS
Rfactor Rfree: 0.3202 / Rfactor Rwork: 0.3505

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