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- PDB-6duj: Crystal structure of A51V variant of Human Cytochrome c -

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Basic information

Entry
Database: PDB / ID: 6duj
TitleCrystal structure of A51V variant of Human Cytochrome c
ComponentsCytochrome c
KeywordsAPOPTOSIS / peroxidase activity / heme
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 / 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 / cellular respiration ...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 / 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 / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Detoxification of Reactive Oxygen Species / : / Pyroptosis / 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 / nucleus / 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
HEME C / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82202726164 Å
AuthorsLei, H. / Bowler, B.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1609720 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P20GM103546 United States
CitationJournal: J.Phys.Chem.B / Year: 2019
Title: Naturally Occurring A51V Variant of Human CytochromecDestabilizes the Native State and Enhances Peroxidase Activity.
Authors: Lei, H. / Bowler, B.E.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5744
Polymers23,3372
Non-polymers1,2372
Water1,63991
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2872
Polymers11,6691
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2872
Polymers11,6691
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.380, 184.369, 35.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

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Components

#1: Protein Cytochrome c


Mass: 11668.636 Da / Num. of mol.: 2 / Mutation: A51V
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


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5.5, 40%(w/v) PEG 600 / PH range: 5.5-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.82→33.33 Å / Num. obs: 18770 / % possible obs: 98.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.26 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 24.5
Reflection shellResolution: 1.83→1.89 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.18 / Num. unique obs: 1878 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TY3

5ty3


Resolution: 1.82202726164→33.3231225686 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33795974971
RfactorNum. reflection% reflection
Rfree0.234877671704 1876 10.0085360649 %
Rwork0.184131398811 --
obs0.189334445331 18744 98.6422481844 %
Displacement parametersBiso mean: 35.2155113493 Å2
Refinement stepCycle: LAST / Resolution: 1.82202726164→33.3231225686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 86 91 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01711554480271776
X-RAY DIFFRACTIONf_angle_d1.247559554932390
X-RAY DIFFRACTIONf_chiral_restr0.0554354896036232
X-RAY DIFFRACTIONf_plane_restr0.00851611711256292
X-RAY DIFFRACTIONf_dihedral_angle_d16.63117763471030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.822-1.87130.3171128024641430.2922997576061284X-RAY DIFFRACTION99.5118549512
1.8713-1.92630.3288851483711400.2565302998861263X-RAY DIFFRACTION99.1519434629
1.9263-1.98850.3068415418991450.2322566368081300X-RAY DIFFRACTION98.7021857923
1.9885-2.05960.2634672419021390.2165051610351248X-RAY DIFFRACTION97.5386779184
2.0596-2.1420.2385871077651410.1979124484751268X-RAY DIFFRACTION98.6694677871
2.142-2.23950.2272656123691460.1893412356081312X-RAY DIFFRACTION99.5221843003
2.2395-2.35750.2720879302921430.1896124367021278X-RAY DIFFRACTION99.0934449093
2.3575-2.50520.2626087854561400.1871289388611268X-RAY DIFFRACTION96.8363136176
2.5052-2.69850.2359640982071450.1789799460461296X-RAY DIFFRACTION99.105914718
2.6985-2.970.1980484456921460.1709445327571325X-RAY DIFFRACTION99.3918918919
2.97-3.39930.2333658833081440.1721840515211287X-RAY DIFFRACTION98.0808773132
3.3993-4.28140.1961852145191500.1479176793211344X-RAY DIFFRACTION99.5336442372
4.2814-33.32870.2333875686821540.1887454639121395X-RAY DIFFRACTION97.3601508485

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