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- PDB-3m2f: Crystallographic and Single Crystal Spectral Analysis of the Pero... -

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Basic information

Entry
Database: PDB / ID: 3m2f
TitleCrystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate
ComponentsCytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE / Cytochrome c peroxidase (CCP) / Heme / Hydrogen peroxide / Iron / Metal-binding / Mitochondrion / Organic radical / Peroxidase
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 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Class I peroxidase / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.4 Å
AuthorsMeharenna, Y.T. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2010
Title: Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate.
Authors: Meharenna, Y.T. / Doukov, T. / Li, H. / Soltis, S.M. / Poulos, T.L.
History
DepositionMar 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)34,0263
Polymers33,3151
Non-polymers7112
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.164, 74.824, 51.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial / CCP


Mass: 33315.012 Da / Num. of mol.: 1 / Fragment: UNP residues 71-361 / Mutation: N184R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCP, CCP1, CPO, YKR066C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 19

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 277.2 K / pH: 6
Details: 10uL (350-400uM protein), 22% MPD, 50mM tris phoshate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K

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Data collection

DiffractionMean temperature: 65 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.954
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 78090 / % possible obs: 94.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.56 / % possible all: 95

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Processing

Software
NameClassification
MOSFLMdata reduction
SHELXmodel building
SHELXL-97refinement
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: NONE

Resolution: 1.4→50 Å / Num. parameters: 36595 / Num. restraintsaints: 33137 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rwork0.1156 ---
all0.1156 ---
obs-74172 91 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 2206.93 / Occupancy sum non hydrogen: 2964
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 48 630 3034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0288
X-RAY DIFFRACTIONs_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.052
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.104

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