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

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Basic information

Entry
Database: PDB / ID: 1mkr
TitleCrystal Structure of a Mutant Variant of Cytochrome c Peroxidase (Plate like crystals)
ComponentsCytochrome c Peroxidase
KeywordsOXIDOREDUCTASE / cytochrome c peroxidase / oxygen radical / Trp cation radical / Trp-Tyr covalent cross-link
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 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 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 400COMPOUND THIS FORM OF CRYSTALS WERE PLATE LIKE, QUITE DIFFERENT FROM THE REGULAR CHUNKY FORM OF CCP. ...COMPOUND THIS FORM OF CRYSTALS WERE PLATE LIKE, QUITE DIFFERENT FROM THE REGULAR CHUNKY FORM OF CCP. THEY BELONGED TO THE SAME SPACE GROUP BUT WITH DIFFERENT UNIT CELL PARAMETERS. HELICAL BUNDLE PROTEIN SYNTHESIZED IN THE CYTOPLASM AND TRANSPORTED TO MITOCHODRIAL INTERMEMBRANE SPACE OF YEAST. IN E.COLI, HOWEVER, SYNTHESIZED AND TRANSLOCATED INTO THE PERIPLASM. PROTEIN HAS DISTINCT DISTAL AND PROXIMAL HEME POCKETS. TRP191 IN THE PROXIMAL HEME POCKET ACTS AS A CONDUIT IN ELECTRON TRANSFER WITH ITS REDOX PARTNER, CYTOCHROME C

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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)34,2132
Polymers33,5961
Non-polymers6161
Water7,710428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.480, 50.957, 118.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHelical bundle protein synthesized in the cytoplasm and transported to mitochodrial intermembrane space of yeast. In E.coli, however, synthesized and translocated into the periplasm. Protein has distinct distal and proximal heme pockets. Trp191 in the proximal heme pocket acts as a conduit in electron transfer with its redox partner, cytochrome c

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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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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 buffer, 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: 124 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 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: 1.58→100 Å / Num. obs: 42967 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.602 % / Rmerge(I) obs: 0.049 / Rsym value: 0.044 / Net I/σ(I): 37.19
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.72 / Num. unique all: 1824 / Rsym value: 0.356 / % possible all: 87.9
Reflection
*PLUS
% possible obs: 94.8 % / Num. measured all: 627338
Reflection shell
*PLUS
% possible obs: 87.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: H52Y6 Dataset - PDB Entry - 1MKQ

1mkq


Resolution: 1.58→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
Rfree0.219 2038 -RANDOM
Rwork0.1944 ---
all-42697 --
obs-40622 95.1 %-
Displacement parametersBiso mean: 21.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.58→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 43 428 2855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0048
X-RAY DIFFRACTIONc_angle_d2.245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
1.58-1.640.4091840.404236048.87
1.64-1.70.32142160.299237459.219
1.7-1.780.29412040.241737069.123
1.78-1.870.24141730.207437599.25
1.87-1.990.25761910.206637379.199
1.99-2.140.21282070.198338029.35
2.36-2.70.21922230.193339629.75
2.7-3.40.19412140.1852411210.12
3.4-500.18762210.1622428010.53
Refinement
*PLUS
% reflection Rfree: 4.8 % / Rfactor Rfree: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg2.245

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