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- PDB-7ljx: Oxidized rat cytochrome c mutant (K53Q) -

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Basic information

Entry
Database: PDB / ID: 7ljx
TitleOxidized rat cytochrome c mutant (K53Q)
ComponentsCytochrome c, somatic
KeywordsOXIDOREDUCTASE / oxidative phosphorylation / cytochrome / acetylated lysine / metastasis
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 / Detoxification of Reactive Oxygen Species / Pyroptosis / 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 / Detoxification of Reactive Oxygen Species / Pyroptosis / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / apoptosome / negative regulation of hydrogen peroxide biosynthetic process / positive regulation of cellular respiration / response to carbon monoxide / Regulation of the apoptosome activity / response to gravity / glial cell apoptotic process / response to copper ion / mitochondrial electron transport, cytochrome c to oxygen / hydrogen peroxide metabolic process / mitochondrial electron transport, ubiquinol to cytochrome c / 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 family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
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: 1.31 Å
AuthorsHuttemann, M. / Edwards, B.F.P. / Brunzelle, J.S. / Vaishnav, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM116807 United States
CitationJournal: Cells / Year: 2021
Title: Lysine 53 Acetylation of Cytochrome c in Prostate Cancer: Warburg Metabolism and Evasion of Apoptosis.
Authors: Bazylianska, V. / Kalpage, H.A. / Wan, J. / Vaishnav, A. / Mahapatra, G. / Turner, A.A. / Chowdhury, D.D. / Kim, K. / Morse, P.T. / Lee, I. / Brunzelle, J.S. / Polin, L. / Subedi, P. / ...Authors: Bazylianska, V. / Kalpage, H.A. / Wan, J. / Vaishnav, A. / Mahapatra, G. / Turner, A.A. / Chowdhury, D.D. / Kim, K. / Morse, P.T. / Lee, I. / Brunzelle, J.S. / Polin, L. / Subedi, P. / Heath, E.I. / Podgorski, I. / Marcus, K. / Edwards, B.F.P. / Huttemann, M.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4415
Polymers22,9922
Non-polymers1,4493
Water3,495194
1
A: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3273
Polymers11,4961
Non-polymers8302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1152
Polymers11,4961
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.837, 96.767, 38.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-202-

FC6

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Components

#1: Protein Cytochrome c, somatic


Mass: 11496.242 Da / Num. of mol.: 2 / Mutation: K53Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cycs / Production host: Escherichia coli (E. coli) / References: UniProt: P62898
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6FeN6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: 0.2 - 03mm x 0.1 mm thin plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: JBS1D4: 30% PEG 2K MME, 0.1M Na MES pH 6.5, 0.1M Na Acetate
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.309→48.384 Å / Num. obs: 48257 / % possible obs: 98.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 12.29 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.051 / Rrim(I) all: 0.128 / Rsym value: 0.117 / Net I/σ(I): 12.2
Reflection shellResolution: 1.309→1.332 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.821 / Num. unique obs: 2078 / CC1/2: 0.896 / Rpim(I) all: 0.325 / Rrim(I) all: 0.887 / Rsym value: 0.806 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
AutoProcessdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0Z

5c0z


Resolution: 1.31→48.38 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.028 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2355 4.9 %RANDOM
Rwork0.138 ---
obs0.14 45282 98.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.31→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 99 195 1908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191764
X-RAY DIFFRACTIONr_bond_other_d0.0010.021640
X-RAY DIFFRACTIONr_angle_refined_deg2.2761.9882391
X-RAY DIFFRACTIONr_angle_other_deg1.2362.9393828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5475206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59725.29468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39715322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.621154
X-RAY DIFFRACTIONr_chiral_restr0.1550.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021932
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02338
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_it1.6131.783830
X-RAY DIFFRACTIONr_mcbond_other1.5711.779829
X-RAY DIFFRACTIONr_mcangle_it1.8992.6811034
X-RAY DIFFRACTIONr_mcangle_other1.9022.6841035
X-RAY DIFFRACTIONr_scbond_it2.4712.14934
X-RAY DIFFRACTIONr_scbond_other2.4742.141932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9883.0161357
X-RAY DIFFRACTIONr_long_range_B_refined3.30122.0652129
X-RAY DIFFRACTIONr_long_range_B_other3.0721.6012095
X-RAY DIFFRACTIONr_rigid_bond_restr2.66433404
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.31→1.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 157 -
Rwork0.291 2972 -
obs--89.53 %

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