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- PDB-5df5: The structure of oxidized rat cytochrome c (T28E) at 1.30 angstro... -

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Basic information

Entry
Database: PDB / ID: 5df5
TitleThe structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.
ComponentsCytochrome c, somatic
KeywordsELECTRON TRANSPORT / cytochrome c / oxidized / rat / mutant
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Respiratory electron transport / Pyroptosis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / apoptosome ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Respiratory electron transport / Pyroptosis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / apoptosome / negative regulation of hydrogen peroxide biosynthetic process / positive regulation of cellular respiration / Regulation of the apoptosome activity / hydrogen peroxide metabolic process / glial cell apoptotic process / response to carbon monoxide / mitochondrial electron transport, cytochrome c to oxygen / response to copper ion / mitochondrial electron transport, ubiquinol to cytochrome c / response to gravity / response to ischemia / mitochondrial intermembrane space / response to oxidative stress / electron transfer activity / apoptotic process / heme binding / enzyme binding / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXACYANOFERRATE(3-) / HEME C / Cytochrome c, somatic
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.301 Å
AuthorsEdwards, B.F.P. / Mahapatra, G. / Vaishnav, A.A. / Brunzelle, J.S. / Huttemann, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthNIGMS RO1 089900 United States
Citation
Journal: To Be Published
Title: The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.
Authors: Edwards, B.F.P. / Mahapatra, G. / Vaishnav, A.A. / Brunzelle, J.S. / Huttemann, M.
#1: Journal: Biochemistry / Year: 2010
Title: Phosphomimetic substitution of cytochrome C tyrosine 48 decreases respiration and binding to cardiolipin and abolishes ability to trigger downstream caspase activation.
Authors: Pecina, P. / Borisenko, G.G. / Belikova, N.A. / Tyurina, Y.Y. / Pecinova, A. / Lee, I. / Samhan-Arias, A.K. / Przyklenk, K. / Kagan, V.E. / Huttemann, M.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c, somatic
B: Cytochrome c, somatic
C: Cytochrome c, somatic
D: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,21111
Polymers46,1014
Non-polymers3,1107
Water6,017334
1
A: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1442
Polymers11,5251
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5684
Polymers11,5251
Non-polymers1,0423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3563
Polymers11,5251
Non-polymers8302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1442
Polymers11,5251
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.609, 51.739, 61.748
Angle α, β, γ (deg.)110.01, 93.09, 91.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome c, somatic


Mass: 11525.303 Da / Num. of mol.: 4 / Mutation: T28E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: somatic / Gene: Cycs / Plasmid: pLW01 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P62898
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6FeN6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe sequence of this entry (rat Cytochrome c as found in UNP P62898/CYC_RAT) and and the mouse ...The sequence of this entry (rat Cytochrome c as found in UNP P62898/CYC_RAT) and and the mouse Cytochrome c (P62897/CYC_MOUSE) are identical

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.26 % / Description: 0.2 x 0.3 mm prism
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20 mg/mL protein in water mixed 1:1 with 30% PEG 1500
PH range: 4.5 only

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.301→57.881 Å / Num. all: 95201 / Num. obs: 90455 / % possible obs: 96.59 % / Redundancy: 5.3 % / Biso Wilson estimate: 13.53 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.3
Reflection shellResolution: 1.301→1.335 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.6 / % possible all: 89.38

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSSeptember 26, 2012data reduction
Aimless0.1.29data scaling
PHENIX1.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0Z

5c0z


Resolution: 1.301→57.88 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.145 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17771 4744 5 %RANDOM
Rwork0.14802 ---
obs0.14949 90455 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-1.55 Å20.51 Å2
2--0.1 Å2-0.14 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.301→57.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 211 334 3781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193536
X-RAY DIFFRACTIONr_bond_other_d0.0020.023387
X-RAY DIFFRACTIONr_angle_refined_deg1.8842.0514790
X-RAY DIFFRACTIONr_angle_other_deg1.94137837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93425.294136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59415657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.483158
X-RAY DIFFRACTIONr_chiral_restr0.1310.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.023951
X-RAY DIFFRACTIONr_gen_planes_other0.0340.02793
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4011.6471662
X-RAY DIFFRACTIONr_mcbond_other1.3921.6461661
X-RAY DIFFRACTIONr_mcangle_it1.7932.4812071
X-RAY DIFFRACTIONr_mcangle_other1.7922.4822072
X-RAY DIFFRACTIONr_scbond_it1.8051.8841874
X-RAY DIFFRACTIONr_scbond_other1.8021.8871836
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0712.6672655
X-RAY DIFFRACTIONr_long_range_B_refined2.98714.0484496
X-RAY DIFFRACTIONr_long_range_B_other2.59813.5944375
X-RAY DIFFRACTIONr_rigid_bond_restr17.95936923
X-RAY DIFFRACTIONr_sphericity_free32.9435123
X-RAY DIFFRACTIONr_sphericity_bonded10.85357051
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 303 -
Rwork0.256 6247 -
obs--89.38 %

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