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- PDB-6s8y: Crystal structure of cytochrome c in complex with a sulfonated qu... -

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Basic information

Entry
Database: PDB / ID: 6s8y
TitleCrystal structure of cytochrome c in complex with a sulfonated quinoline-derived foldamer
ComponentsCytochrome c iso-1
KeywordsOXIDOREDUCTASE / Charge interactions / cytochrome c / protein assembly / protein recognition / quinoline foldamer
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / 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 ...Release of apoptotic factors from the mitochondria / Pyroptosis / 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 family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / HEME C / Chem-L0T / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsAlex, J.M. / Corvaglia, V. / Hu, X. / Engilberge, S. / Huc, I. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Crystal structure of a protein-aromatic foldamer composite: macromolecular chiral resolution.
Authors: Alex, J.M. / Corvaglia, V. / Hu, X. / Engilberge, S. / Huc, I. / Crowley, P.B.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0119
Polymers11,9711
Non-polymers5,0408
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-138 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.138, 39.138, 187.366
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-203-

ZN

21A-205-

ACT

31A-205-

ACT

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome c iso-1


Mass: 11970.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044

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Non-polymers , 5 types, 34 molecules

#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-L0T / 8-acetamido-2-[[2-[[2-[[2-[[2-[[2-[[2-[(2-carboxy-4-sulfonato-quinolin-8-yl)carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]-4-sulfonato-quinolin-8-yl]carbamoyl]quinoline-4-sulfonate


Mass: 2053.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C82H44N16O34S8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5 % PEG 3350, 100 mM sodium acetate pH 4.5, 200 mM zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.09→62.45 Å / Num. obs: 10590 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.02 / Rrim(I) all: 0.084 / Net I/σ(I): 19
Reflection shellResolution: 2.09→2.12 Å / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10386 / Rpim(I) all: 0.283 / Rrim(I) all: 1.273 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LYC

5lyc


Resolution: 2.09→33.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.258 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.197
RfactorNum. reflection% reflectionSelection details
Rfree0.267 498 4.7 %RANDOM
Rwork0.225 ---
obs0.227 10589 100 %-
Displacement parametersBiso max: 145.18 Å2 / Biso mean: 67.41 Å2 / Biso min: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.1953 Å20 Å20 Å2
2---3.1953 Å20 Å2
3---6.3906 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.09→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 480 26 1347
Biso mean--61.95 69.78 -
Num. residues----107
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d413SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes214HARMONIC5
X-RAY DIFFRACTIONt_it1398HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion108SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1294SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1398HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1993HARMONIC21.52
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion18.61
LS refinement shellResolution: 2.09→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.3763 26 5.88 %
Rwork0.2495 416 -
all0.2581 442 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.12351.9991.04836.90442.07769.9693-0.1821-0.0240.5963-0.4808-0.05460.2037-0.3181-0.86380.2367-0.27270.0093-0.00160.0341-0.1303-0.17212.83354.214116.9803
24.4472-3.98063.222915.5345-7.56289.66640.071-0.1126-0.13960.1562-0.3157-0.08110.30370.35740.2446-0.221-0.06990.0513-0.24780.0418-0.13684.091-25.146626.4268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 103
2X-RAY DIFFRACTION2A206 - 208

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