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- PDB-1ml2: Crystal Structure of a Mutant Variant of Cytochrome c Peroxidase ... -

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Basic information

Entry
Database: PDB / ID: 1ml2
TitleCrystal Structure of a Mutant Variant of Cytochrome c Peroxidase with Zn(II)-(20-oxo-Protoporphyrin IX)
ComponentsCytochrome c Peroxidase
KeywordsOXIDOREDUCTASE / Cytochrome c peroxidase / ZnCcP / Zn-Protoporphyrin IX / oxygen radical / Trp cation radical / Trp-Tyr Covalent Cross-link
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
20-OXO-PROTOPORPHYRIN IX CONTAINING ZN(II) / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBhaskar, B. / Immoos, C.E. / Shimizu, H. / Farmer, P.J. / Poulos, T.L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A Novel Heme and Peroxide-Dependent Tryptophan-Tyrosine Cross-Link in a Mutant of Cytochrome c Peroxidase
Authors: Bhaskar, B. / Immoos, C.E. / Shimizu, H. / Sulc, F. / Farmer, P.J. / Poulos, T.L.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral
Remark 400COMPOUND ZN(II)-PROTOPORPHYRIN IX INCORPORATED INTO H52Y MUTANT OF CCP. IN THE PRESENCE OF REDOX ...COMPOUND ZN(II)-PROTOPORPHYRIN IX INCORPORATED INTO H52Y MUTANT OF CCP. IN THE PRESENCE OF REDOX INACTIVE ZN-PORPHRIN NO TRP-TYR COVALENT CROSS-LINK.

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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)34,2382
Polymers33,5961
Non-polymers6421
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.487, 50.998, 118.759
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 / CCP


Mass: 33596.266 Da / Num. of mol.: 1 / Mutation: H52Y
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-ZEM / 20-OXO-PROTOPORPHYRIN IX CONTAINING ZN(II) / ZN(II)-(20-OXO-PROTOPORPHYRIN IX)


Mass: 642.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32N4O5Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-Methyl-2,4-Pentanediol (MPD), tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
250 mMKPB1dropor Tris-phosphate, pH6.0
318 %MPD1drop
430 %MPD1reservoir

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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: Oct 24, 2001
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. obs: 34532 / % possible obs: 91.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.74 % / Rmerge(I) obs: 0.044 / Rsym value: 0.051 / Net I/σ(I): 44.47
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.67 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 11.36 / Num. unique all: 1614 / Rsym value: 0.121 / % possible all: 86.8
Reflection
*PLUS
% possible obs: 91.2 % / Num. measured all: 434384
Reflection shell
*PLUS
% possible obs: 86.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-GENdata reduction
AMoREphasing
CNS1.1refinement
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry : 1MK8 - H52Y1 Structure

1mk8


Resolution: 1.65→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
Rfree0.2151 1741 -RANDOM
Rwork0.1831 ---
all-37716 --
obs-34380 91.2 %-
Displacement parametersBiso mean: 18.5538 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 44 506 2934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0048
X-RAY DIFFRACTIONc_angle_d1.18
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.65-1.710.27131600.3052X-RAY DIFFRACTION30578.891
1.71-1.780.26361790.2459X-RAY DIFFRACTION30598.897
1.78-1.860.2031410.1972X-RAY DIFFRACTION30979.008
1.86-1.960.24281790.1985X-RAY DIFFRACTION31199.072
1.96-2.080.20871740.1841X-RAY DIFFRACTION31909.27
2.08-2.240.21381530.1874X-RAY DIFFRACTION32739.52
2.24-2.460.2271850.1868X-RAY DIFFRACTION32919.57
2.46-2.820.2341950.1876X-RAY DIFFRACTION34209.94
2.82-3.550.1881850.1639X-RAY DIFFRACTION350710.2
3.55-500.19891900.1615X-RAY DIFFRACTION362610.54
Refinement
*PLUS
% reflection Rfree: 4.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.18

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