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- PDB-5kke: Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytoch... -

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Basic information

Entry
Database: PDB / ID: 5kke
TitleCrystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with CYMAL5
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT / Electron Transport Apoptosis Lipid Binding
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / 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
HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 1.701 Å
AuthorsBowler, B.E. / Whitby, F.G.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons.
Authors: McClelland, L.J. / Steele, H.B. / Whitby, F.G. / Mou, T.C. / Holley, D. / Ross, J.B. / Sprang, S.R. / Bowler, B.E.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _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_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5258
Polymers12,0001
Non-polymers1,5257
Water1,42379
1
A: Cytochrome c iso-1
hetero molecules

A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,04916
Polymers23,9992
Non-polymers3,05014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area9370 Å2
ΔGint-159 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.740, 69.326, 72.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-362-

HOH

31A-364-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome c iso-1


Mass: 11999.667 Da / Num. of mol.: 1 / Mutation: K72A, C102S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00044

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Non-polymers , 6 types, 86 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservior solution: 77% Ammonium Sulfate, 0.1 M Tris, pH 7.5 Protein Solution: 18 mg/mL in 75 % Ammonium Sulfate Detergent Solution: 2.5 mM CYMAL-5 in deionized water Mixed 2:2:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2016 / Details: Varimax-HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 26560 / % possible obs: 99.9 % / Redundancy: 14.7 % / Biso Wilson estimate: 26.78 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.015 / Rrim(I) all: 0.06 / Χ2: 1.023 / Net I/av σ(I): 44.633 / Net I/σ(I): 16 / Num. measured all: 389670
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7611.30.9326420.8290.2840.9740.91799.5
1.76-1.8314.20.58326290.950.1610.6050.962100
1.83-1.9114.60.38526870.9750.1040.3991.095100
1.91-2.0214.70.26926440.9870.0720.2781.082100
2.02-2.1414.90.18526620.9930.050.1911.05100
2.14-2.31150.13526620.9960.0360.1391.005100
2.31-2.5415.20.09126490.9980.0240.0940.982100
2.54-2.9115.40.06426720.9990.0170.0660.968100
2.91-3.6615.60.042264410.0110.0441.059100
3.66-4015.70.033266910.0090.0341.08299.9

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å26.98 Å
Translation3 Å26.98 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
CrystalCleardata collection
SCALEPACKdata scaling
PHASER2.6.0phasing
SOLVEphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 1.701→26.981 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 2654 9.99 %
Rwork0.1708 23901 -
obs0.1742 26555 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.72 Å2 / Biso mean: 38.6617 Å2 / Biso min: 16.9 Å2
Refinement stepCycle: final / Resolution: 1.701→26.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 134 79 1056
Biso mean--38.88 44.31 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091038
X-RAY DIFFRACTIONf_angle_d1.041411
X-RAY DIFFRACTIONf_chiral_restr0.051148
X-RAY DIFFRACTIONf_plane_restr0.006165
X-RAY DIFFRACTIONf_dihedral_angle_d19.742579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7011-1.73210.40621340.34331236137098
1.7321-1.76540.27721340.25212531387100
1.7654-1.80140.25261320.216812661398100
1.8014-1.84050.28461540.220512351389100
1.8405-1.88340.24861230.196312661389100
1.8834-1.93040.22661460.184512911437100
1.9304-1.98260.21191500.173712381388100
1.9826-2.04090.20281300.1712491379100
2.0409-2.10680.21941330.159612561389100
2.1068-2.18210.19121650.16412441409100
2.1821-2.26940.21491330.164312621395100
2.2694-2.37260.18841380.167712851423100
2.3726-2.49760.22451380.166412421380100
2.4976-2.6540.19881330.164512831416100
2.654-2.85870.19531450.184112371382100
2.8587-3.1460.24141480.17712721420100
3.146-3.60030.2161370.170512431380100
3.6003-4.53250.17171390.142812771416100
4.5325-26.98470.17441420.170312661408100
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)
16.1127-5.39413.66686.2593-4.89874.6570.44652.0866-0.5076-0.1378-0.8928-1.00750.20241.81360.47680.5614-0.09760.07890.887-0.14270.619325.370915.548485.2646
27.41645.13971.8093.7740.47843.5826-0.18520.05020.416-0.39610.03240.2728-0.68670.35630.10590.4122-0.076-0.00080.2183-0.01670.27058.67117.796385.0655
36.66870.736-0.28066.46830.20634.8196-0.0743-0.42360.35140.34550.03680.2373-0.30120.18730.05470.2137-0.0108-0.01010.1849-0.0420.20825.84927.029793.0004
42.19971.5092-0.34016.21-1.575.7446-0.1785-0.1651-0.12040.13730.0961-0.69050.42630.75270.01360.22680.0671-0.02990.31-0.01920.337110.9832-4.650991.2256
58.20211.61464.33045.0770.82518.4175-0.1978-0.0181-0.1011-0.20860.1616-0.60850.11490.81790.00290.22620.0240.050.4083-0.06420.312816.21861.596782.5339
64.0374-4.7637-3.95627.20533.33835.3901-0.0238-0.4833-0.12880.68020.4734-0.19040.77260.887-0.36630.49550.1448-0.06910.44-0.08530.410614.0212-11.732267.9637
76.2671-4.04324.63873.0278-3.37543.78950.0007-0.0179-0.17470.00860.2747-0.29350.31140.6314-0.33780.40980.13920.00690.3692-0.09440.309915.5162-15.113353.8999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID -4:1)A-4 - 1
2X-RAY DIFFRACTION2(CHAIN A AND RESID 2:15)A2 - 15
3X-RAY DIFFRACTION3(CHAIN A AND RESID 16:36)A16 - 36
4X-RAY DIFFRACTION4(CHAIN A AND RESID 37:54)A37 - 54
5X-RAY DIFFRACTION5(CHAIN A AND RESID 55:78)A55 - 78
6X-RAY DIFFRACTION6(CHAIN A AND RESID 79:91)A79 - 91
7X-RAY DIFFRACTION7(CHAIN A AND RESID 92:103)A92 - 103

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