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- PDB-4ye1: A cytochrome c plus calixarene structure - alternative ligand bin... -

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Basic information

Entry
Database: PDB / ID: 4ye1
TitleA cytochrome c plus calixarene structure - alternative ligand binding mode
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / protein surface recognition / lysine binding
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding
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
HEME C / Chem-T3Y / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsMallon, M.M. / McGovern, R.E. / McCarty, A.A. / Crowley, P.B.
CitationJournal: To Be Published
Title: A cytochrome c-calixarene structure
Authors: Mallon, M.M. / McGovern, R.E. / McCarty, A.A. / Crowley, P.B.
History
DepositionFeb 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c iso-1
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6558
Polymers24,0922
Non-polymers3,5636
Water7,602422
1
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4093
Polymers12,0461
Non-polymers1,3632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2465
Polymers12,0461
Non-polymers2,2004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.850, 56.070, 108.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome c iso-1


Mass: 12045.755 Da / Num. of mol.: 2 / Mutation: R13E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CYC1, YJR048W, J1653 / Plasmid: pBTR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00044
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-T3Y / 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid / 5,11,17,23-tetra-sulphonato-calix[4]arene-25,26,27,28-tetrol


Mass: 744.741 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H24O16S4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.392→108 Å / Num. all: 44554 / Num. obs: 44554 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.095 / Rsym value: 0.088 / Net I/av σ(I): 6.527 / Net I/σ(I): 14.6 / Num. measured all: 321450
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.39-1.477.10.4181.84551163950.1680.4184.6100
1.47-1.567.20.292.64407560860.1160.296.4100
1.56-1.667.30.2093.64148857050.0830.2098.4100
1.66-1.87.30.1553888853380.060.1511100
1.8-1.977.30.10573586749160.0410.10514.9100
1.97-2.27.30.06910.43264444780.0270.06920.2100
2.2-2.547.30.06510.42908240000.0260.06522.7100
2.54-3.117.20.0728.62447533860.0290.07226.6100
3.11-4.47.10.05311.31905726830.0210.05332100
4.4-26.3546.60.03815.31036315670.0160.03830.399.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.36 Å
Translation2.5 Å26.36 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TYI

3tyi


Resolution: 1.39→26.38 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.636 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1597 2245 5 %RANDOM
Rwork0.1303 ---
obs0.1318 42297 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 339.31 Å2 / Biso mean: 10.634 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0 Å2
2---0.14 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 1.39→26.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 236 422 2348
Biso mean--8.85 31.25 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192124
X-RAY DIFFRACTIONr_bond_other_d0.0040.021944
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9512943
X-RAY DIFFRACTIONr_angle_other_deg1.162.9524537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74525.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.47154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022363
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02469
X-RAY DIFFRACTIONr_mcbond_it0.7540.718907
X-RAY DIFFRACTIONr_mcbond_other0.750.716906
X-RAY DIFFRACTIONr_mcangle_it0.9211.0791139
X-RAY DIFFRACTIONr_rigid_bond_restr14.31934068
X-RAY DIFFRACTIONr_sphericity_free30.968571
X-RAY DIFFRACTIONr_sphericity_bonded17.85454338
LS refinement shellResolution: 1.392→1.428 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 179 -
Rwork0.172 3073 -
all-3252 -
obs--100 %

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