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- PDB-1bek: EFFECT OF UNNATURAL HEME SUBSTITUTION ON KINETICS OF ELECTRON TRA... -

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Basic information

Entry
Database: PDB / ID: 1bek
TitleEFFECT OF UNNATURAL HEME SUBSTITUTION ON KINETICS OF ELECTRON TRANSFER IN CYTOCHROME C PEROXIDASE
ComponentsYEAST CYTOCHROME C PEROXIDASE
KeywordsPEROXIDASE / OXIDOREDUCTASE
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 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMiller, M.A. / Kraut, J.
Citation
Journal: To be Published
Title: Effect of Unnatural Heme Substitution on Kinetics of Electron Transfer in Cytochrome C Peroxidase
Authors: Miller, M.A. / Millett, F. / Durham, B. / Kraut, J. / Mei, H.K. / Ashford, V.A. / Xuong, N.-H. / Kraut, J.
#1: Journal: Biochemistry / Year: 1990
Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme-Cleft Mutants Prepared by Site-Directed Mutagenesis
Authors: Wang, J.M. / Mauro, M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.H. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7-A Resolution
Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J.
History
DepositionMay 16, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YEAST CYTOCHROME C PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7512
Polymers33,1351
Non-polymers6161
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.018, 74.206, 45.478
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 YEAST CYTOCHROME C PEROXIDASE


Mass: 33134.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE NATURALLY OCCURRING PROTOHEME REPLACED BY MESOHEME (2,4-CH2-CH3 PORPHYRIN)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENZYME WAS PURIFIED IN THE APO FORM, THEN RECONSTITUTED WITH THE UNNATURAL MESOHEME PROSTHETIC ...THIS ENZYME WAS PURIFIED IN THE APO FORM, THEN RECONSTITUTED WITH THE UNNATURAL MESOHEME PROSTHETIC GROUP. THE SUBSTITUTION SHIFTED THE ABSORPTION SPECTRUM MAXIMA ABOUT 8 NM TO THE BLUE.
Sequence detailsTHIS CYTOCHROME C PEROXIDASE DIFFERS FROM THE PREVIOUSLY DEPOSITED STRUCTURE (PROTEIN DATA BANK ...THIS CYTOCHROME C PEROXIDASE DIFFERS FROM THE PREVIOUSLY DEPOSITED STRUCTURE (PROTEIN DATA BANK ENTRY 2CYP) BY TWO STRAIN-RELATED SEQUENCE DIFFERENCES: THR 53 TO ILE AND ASP 152 TO GLY, AND THE ADDITION OF MET-ILE AT THE N-TERMINUS, HENCE CCP(MI). THE OVERALL STRUCTURE IS THE SAME AS THE PREVIOUSLY DEPOSITED ONE BUT IN A DIFFERENT CELL PACKING. RESIDUES ARE NUMBERED TO BE CONSISTENT WITH THE SEQUENCE OF THE NATIVE (2CYP) STRUCTURE. THUS THE FIRST TWO RESIDUES HAVE RESIDUE NUMBERS -1 AND 0, RESPECTIVELY. THE NATIVE STRUCTURE IS AVAILABLE FROM THE PDB AS ENTRY 1CCP AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS, CCP(MI,W51F), CCP(MI,W191F), AND CCP(MI,D235N), ARE ALSO AVAILABLE FROM THE PROTEIN DATA BANK AS ENTRIES 2CCP, 3CCP, AND 4CPP, RESPECTIVELY.

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growpH: 6 / Details: 50 MM POTASSIUM PHOSPHATE; 30% MPD, pH 6

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 17694 / % possible obs: 95 % / Observed criterion σ(I): 2 / Rsym value: 0.08421
Reflection shellHighest resolution: 2.2 Å / Mean I/σ(I) obs: 2.15 / Rsym value: 0.17

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.2→20 Å
Details: THE SOLUTION WAS OBTAINED USING A>B>C AS THE UNIT CELL PARAMETERS. COORDINATES FOR RESIDUES -1, 0 AND 1 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE ...Details: THE SOLUTION WAS OBTAINED USING A>B>C AS THE UNIT CELL PARAMETERS. COORDINATES FOR RESIDUES -1, 0 AND 1 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. ALTHOUGH COORDINATES FOR RESIDUE 2 ARE INCLUDED, THEY ARE NOT WELL DEFINED DUE TO VERY LARGE TEMPERATURE FACTORS (OVER 100 ANGSTROMS SQUARED).
RfactorNum. reflection% reflection
all0.165 --
obs-17709 95 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 43 164 2512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.523
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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