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- PDB-1bj9: EFFECT OF UNNATURAL HEME SUBSTITUTION ON KINETICS OF ELECTRON TRA... -

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Basic information

Entry
Database: PDB / ID: 1bj9
TitleEFFECT OF UNNATURAL HEME SUBSTITUTION ON KINETICS OF ELECTRON TRANSFER IN CYTOCHROME C PEROXIDASE
ComponentsCYTOCHROME C PEROXIDASE
KeywordsOXIDOREDUCTASE / 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
Chem-DDH / 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. / Wei, 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. / Mauro, J.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
DepositionJul 3, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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_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 1.4Feb 7, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_chiral

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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)33,8752
Polymers33,2271
Non-polymers6481
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.197, 74.364, 45.402
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


Mass: 33226.922 Da / Num. of mol.: 1 / Mutation: T53I, D152G, N272D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase
#2: Chemical ChemComp-DDH / [7,12-DEACETYL-3,8,13,17-TETRAMETHYL-21H,23H-PORPHINE-2,18-DIPROPANOATO(2-)-N21,N22,N23,N24]-IRON / DIACETYLDEUTEROHEME


Mass: 648.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
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. THE NATIVE STRUCTURE IS AVAILABLE FROM THE PROTEIN DATA BANK AS ENTRY 1CCP AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENSIS, 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: pH 6

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorDetector: AREA DETECTOR / Date: Jun 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: 24668 / % possible obs: 98 % / Observed criterion σ(I): 2 / Rsym value: 0.067
Reflection shellHighest resolution: 2.2 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.197

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Processing

SoftwareName: TNT / Version: 1 / Classification: refinement
RefinementResolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 2.16 / Stereochemistry target values: TNT PROTGEO /
RfactorNum. reflection% reflection
obs0.179 24668 99.4 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 45 179 2516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.648
X-RAY DIFFRACTIONt_dihedral_angle_d15.918
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.024
X-RAY DIFFRACTIONt_gen_planes0.006
X-RAY DIFFRACTIONt_it4.833
X-RAY DIFFRACTIONt_nbd0.025

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