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Basic information

Entry
Database: PDB / ID: 2bcn
TitleSolvent isotope effects on interfacial protein electron transfer between cytochrome c and cytochrome c peroxidase
Components
  • Cytochrome c iso-1
  • cytochrome c peroxidase
KeywordsOXIDOREDUCTASE/ELECTRON TRANSFER / protein-protein complex / OXIDOREDUCTASE-ELECTRON TRANSFER COMPLEX
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / response to reactive oxygen species ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 / 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 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / PROTOPORPHYRIN IX CONTAINING ZN / : / Cytochrome c isoform 1 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKang, S.A. / Crane, B.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Solvent isotope effects on interfacial protein electron transfer in crystals and electrode films.
Authors: Kang, S.A. / Hoke, K.R. / Crane, B.R.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cytochrome c peroxidase
B: Cytochrome c iso-1
C: cytochrome c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4686
Polymers79,5973
Non-polymers1,8713
Water9,854547
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.533, 47.089, 84.289
Angle α, β, γ (deg.)102.47, 98.74, 102.16
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: THR / End label comp-ID: ZNH / Refine code: 5 / Auth seq-ID: 1 - 295 / Label seq-ID: 3 - 1

Dom-IDAuth asym-IDLabel asym-ID
1AA - D
2CC - E

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Components

#1: Protein cytochrome c peroxidase /


Mass: 33769.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
References: GenBank: 171177, UniProt: P00431*PLUS, cytochrome-c peroxidase
#2: Protein Cytochrome c iso-1


Mass: 12057.770 Da / Num. of mol.: 1 / Mutation: C107S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CYC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044
#3: Chemical ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN


Mass: 626.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32N4O4Zn
#4: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG3350, NaCl, BOG, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 70156 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.76 Å / % possible all: 67

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.61 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.31 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3335 5.1 %RANDOM
Rwork0.219 ---
all0.219 144954 --
obs0.219 65527 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.329 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5589 0 129 547 6265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0225898
X-RAY DIFFRACTIONr_angle_refined_deg2.9672.0038012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5295693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.09824.881293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65915962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8211523
X-RAY DIFFRACTIONr_chiral_restr0.2620.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.024629
X-RAY DIFFRACTIONr_nbd_refined0.2720.22773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3260.2434
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4450.2145
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5880.239
X-RAY DIFFRACTIONr_mcbond_it0.8221.53551
X-RAY DIFFRACTIONr_mcangle_it1.29325539
X-RAY DIFFRACTIONr_scbond_it2.17932757
X-RAY DIFFRACTIONr_scangle_it3.0924.52467
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberRmsTypeWeight
11760.34MEDIUM POSITIONAL0.5
12380.63LOOSE POSITIONAL5
11761.1MEDIUM THERMAL2
12381.7LOOSE THERMAL10
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.326 154
Rwork0.293 3145
all-3299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.74941.4212-3.69558.4413-3.718923.2994-0.477-1.8371-0.58220.9642-0.00620.28910.91950.22060.48330.2905-0.03480.12550.29160.09070.2186-9.7333-10.22317.6757
21.5285-0.8376-0.8081.9090.85281.690.03270.0671-0.095-0.087-0.04460.06050.0501-0.1220.012-0.1205-0.0094-0.0159-0.13450.0288-0.131513.5516-28.233339.4226
31.78930.0869-0.45961.5530.5782.00060.0363-0.07170.10780.02460.01150.0028-0.08180.0176-0.0478-0.14230.0132-0.0094-0.1390.0052-0.13833.9123.6068-6.5645
40.025-0.05610.1540.126-0.34550.94780.0232-0.01-0.00020.01080.00720.0276-0.018-0.0647-0.03050.07620.0041-0.00350.091-0.02890.13838.4004-10.279914.0797
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11BB1 - 1081 - 108
21BF1091
32CC1 - 2943 - 296
42CE2951
53AA1 - 2943 - 296
63AD2951
74AG1001 - 15471 - 286

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