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- PDB-5o10: Y48H mutant of human cytochrome c -

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Basic information

Entry
Database: PDB / ID: 5o10
TitleY48H mutant of human cytochrome c
ComponentsCytochrome c
KeywordsELECTRON TRANSFER / APOPTOSIS / Heme / haem / cytochrome c / metalloprotein
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: 1.36 Å
AuthorsMoreno-Chicano, T. / Deacon, O.M. / Hough, M.A. / Worrall, J.A.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2013-164 United Kingdom
CitationJournal: Biochemistry / Year: 2017
Title: Heightened Dynamics of the Oxidized Y48H Variant of Human Cytochrome c Increases Its Peroxidatic Activity.
Authors: Deacon, O.M. / Karsisiotis, A.I. / Moreno-Chicano, T. / Hough, M.A. / Macdonald, C. / Blumenschein, T.M.A. / Wilson, M.T. / Moore, G.R. / Worrall, J.A.R.
History
DepositionMay 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4684
Polymers23,2312
Non-polymers1,2372
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-52 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.937, 36.498, 60.700
Angle α, β, γ (deg.)90.000, 116.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c /


Mass: 11615.556 Da / Num. of mol.: 2 / Mutation: Y48H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYCS, CYC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P99999
#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 33% PEG 6000 100mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2016 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.36→54.25 Å / Num. obs: 45812 / % possible obs: 95.3 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Net I/av σ(I): 13.3 / Net I/σ(I): 13.3
Reflection shellResolution: 1.36→1.39 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2124 / CC1/2: 0.51 / Rpim(I) all: 0.51 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zcf

3zcf


Resolution: 1.36→54.25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.963 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.052
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.175 2362 5.2 %RANDOM
Rwork0.1443 ---
obs0.146 43449 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.31 Å2 / Biso mean: 18.567 Å2 / Biso min: 8.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.37 Å2
2--0.44 Å20 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.36→54.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 86 214 1928
Biso mean--10.96 30.18 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021800
X-RAY DIFFRACTIONr_bond_other_d0.0020.021715
X-RAY DIFFRACTIONr_angle_refined_deg2.1792.0872434
X-RAY DIFFRACTIONr_angle_other_deg2.6043.0014009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11924.84866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.496155
X-RAY DIFFRACTIONr_chiral_restr0.090.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021973
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02324
X-RAY DIFFRACTIONr_rigid_bond_restr2.1133515
X-RAY DIFFRACTIONr_sphericity_free22.2795152
X-RAY DIFFRACTIONr_sphericity_bonded7.51553524
LS refinement shellResolution: 1.362→1.397 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 162 -
Rwork0.3 3043 -
all-3205 -
obs--91.18 %

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