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- PDB-6xnk: Crystal structure of dimeric K72A human cytochrome c alkaline con... -

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Basic information

Entry
Database: PDB / ID: 6xnk
TitleCrystal structure of dimeric K72A human cytochrome c alkaline conformer
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / cytochrome c / cardiolipin / heme protein
Function / homology
Function and homology information


Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Detoxification of Reactive Oxygen Species / Pyroptosis / respirasome / intrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / Cytoprotection by HMOX1 / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding / nucleus / 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
HEME C / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsLei, H. / Bowler, B.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1609720 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Alkaline State of the Domain-Swapped Dimer of Human Cytochrome c : A Conformational Switch for Apoptotic Peroxidase Activity.
Authors: Lei, H. / Kelly, A.D. / Bowler, B.E.
History
DepositionJul 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
C: Cytochrome c
E: Cytochrome c
G: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8048
Polymers46,3304
Non-polymers2,4744
Water1,964109
1
A: Cytochrome c
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4024
Polymers23,1652
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-90 kcal/mol
Surface area10990 Å2
MethodPISA
2
E: Cytochrome c
G: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4024
Polymers23,1652
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-87 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.660, 49.595, 61.556
Angle α, β, γ (deg.)77.967, 79.015, 90.189
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 104 / Label seq-ID: 1 - 104

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A'AA
2chain 'C'CB
3chain 'E'EC
4chain 'G'GD

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Components

#1: Protein
Cytochrome c /


Mass: 11582.479 Da / Num. of mol.: 4 / Mutation: K72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYCS, CYC / Production host: Escherichia coli (E. coli) / References: UniProt: P99999
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.9 / Details: 30% MPD, 0.1 M CHES pH 9.9 / PH range: 9-9.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.08→42.12 Å / Num. obs: 22075 / % possible obs: 90.5 % / Redundancy: 3 % / Biso Wilson estimate: 28.4888322735 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.05
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 1757 / % possible all: 72.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ty3

5ty3


Resolution: 2.08→42.11 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2335 1999 9.1 %
Rwork0.1763 --
obs0.1815 22029 90.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.9 Å2
Refinement stepCycle: LAST / Resolution: 2.08→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 172 109 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01556359476753524
X-RAY DIFFRACTIONf_angle_d1.405316468064744
X-RAY DIFFRACTIONf_chiral_restr0.0601754552352460
X-RAY DIFFRACTIONf_plane_restr0.00783535417458580
X-RAY DIFFRACTIONf_dihedral_angle_d15.90010869072036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0804-2.13230.30031120.21821115X-RAY DIFFRACTION71.0069444444
2.1323-2.190.2710707466171340.2111400399161349X-RAY DIFFRACTION85.2298850575
2.19-2.25440.3093085286971460.2159435184221438X-RAY DIFFRACTION90.1023890785
2.2544-2.32720.2903292901561440.2004232665211455X-RAY DIFFRACTION93.5087719298
2.3272-2.41040.2608172582011490.1812678133231485X-RAY DIFFRACTION93.5317687464
2.4104-2.50680.2604290350421450.1861144483321464X-RAY DIFFRACTION93.3294663573
2.5068-2.62090.2405383858891480.1678313170091489X-RAY DIFFRACTION93.5428571429
2.6209-2.75910.2313996408211440.1748634282391433X-RAY DIFFRACTION91.2615740741
2.7591-2.93190.2272345662141450.1645133713031462X-RAY DIFFRACTION91.566951567
2.9319-3.15820.2121111090671470.1733848075611466X-RAY DIFFRACTION95.6702253855
3.1582-3.47590.2095905219621500.1590939446031519X-RAY DIFFRACTION94.8834565094
3.4759-3.97850.2354524458071450.1670421623911444X-RAY DIFFRACTION91.6378316032
3.9785-5.01120.1986510026281460.150331716431472X-RAY DIFFRACTION92.4043403769
5.0112-42.110.2348223134771440.2011439294491439X-RAY DIFFRACTION91.8746372606

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