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

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Basic information

Entry
Database: PDB / ID: 5klu
TitleCrystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with omega-undecylenyl-beta-D-maltopyranoside
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
omega-undecylenyl-beta-D-maltopyranoside / HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsBowler, B.E. / Whitby, F.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1306903 United States
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 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / 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 / _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 / _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 / _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_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_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

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)26,14910
Polymers23,5392
Non-polymers2,6108
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-136 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.489, 61.438, 74.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-322-

HOH

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Components

#1: Protein Cytochrome c iso-1


Mass: 11769.448 Da / Num. of mol.: 2 / 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) / References: UniProt: P00044
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-6UZ / omega-undecylenyl-beta-D-maltopyranoside / (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-4,5-bis(oxidanyl )-6-undec-10-enoxy-oxan-3-yl]oxy-oxane-3,4,5-triol


Mass: 494.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H42O11
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservior: 90% ammonium sulfate, 0.1 M Tris, pH 7.5 Protein: 8 mg/mL in 75% ammonium sulfate Detergent: 12 mM w-undecylenyl-b-D-maltopyranoside in deionized water Mixed 2:2:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 5, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→37.43 Å / Num. obs: 17478 / % possible obs: 99.7 % / Redundancy: 22.7 % / Biso Wilson estimate: 40.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.044 / Rrim(I) all: 0.263 / Net I/σ(I): 23.3 / Num. measured all: 397044 / Scaling rejects: 2620
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0515.11.8191903612610.7620.4731.8811.698
8.94-37.4330.50.05472892390.9990.0110.05592.998.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.96 Å27.24 Å
Translation2.96 Å27.24 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.25data scaling
Blu-Ice5data collection
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→37.083 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 3916 12.1 %
Rwork0.2008 28452 -
obs0.2073 32368 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.67 Å2 / Biso mean: 81.3354 Å2 / Biso min: 22.75 Å2
Refinement stepCycle: final / Resolution: 1.99→37.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 174 37 1840
Biso mean--80.17 50.01 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091885
X-RAY DIFFRACTIONf_angle_d0.9572551
X-RAY DIFFRACTIONf_chiral_restr0.053254
X-RAY DIFFRACTIONf_plane_restr0.006306
X-RAY DIFFRACTIONf_dihedral_angle_d18.1331078
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9896-2.01390.3138710.310253961051
2.0139-2.03940.29351380.249610401178100
2.0394-2.06620.32631460.23911022116899
2.0662-2.09450.22051420.248910521194100
2.0945-2.12440.28191320.218910111143100
2.1244-2.15610.3031470.207210601207100
2.1561-2.18980.27421430.22151016115999
2.1898-2.22570.27171400.230410391179100
2.2257-2.26410.23821420.207510441186100
2.2641-2.30520.24721400.227110161156100
2.3052-2.34960.30531490.20981041119099
2.3496-2.39750.26321410.208810371178100
2.3975-2.44960.21331380.195610131151100
2.4496-2.50660.21221450.179110371182100
2.5066-2.56930.22511410.17811046118799
2.5693-2.63870.21821430.18021026116999
2.6387-2.71640.2221410.188210181159100
2.7164-2.8040.25981350.191110441179100
2.804-2.90420.22961490.204410591208100
2.9042-3.02040.27611430.219310101153100
3.0204-3.15780.29481490.21011028117799
3.1578-3.32420.21141420.203910251167100
3.3242-3.53230.26811430.192610361179100
3.5323-3.80480.26351450.20210451190100
3.8048-4.18720.27561430.197610381181100
4.1872-4.7920.26581420.170510351177100
4.792-6.03320.24651430.200810411184100
6.0332-37.08890.2551430.211210341177100
Refinement TLS params.Method: refined / Origin x: -11.087 Å / Origin y: 4.3674 Å / Origin z: -18.2492 Å
111213212223313233
T0.523 Å20.0188 Å2-0.1008 Å2-0.4236 Å20.0838 Å2--0.3976 Å2
L2.2731 °2-0.2984 °20.1137 °2-2.8025 °20.6568 °2--2.3656 °2
S0.0038 Å °0.6272 Å °0.1675 Å °-0.8275 Å °-0.0222 Å °0.4874 Å °-0.5312 Å °-0.3209 Å °-0.2588 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 105
2X-RAY DIFFRACTION1allB-3 - 105
3X-RAY DIFFRACTION1allC101
4X-RAY DIFFRACTION1allC102
5X-RAY DIFFRACTION1allD1 - 4
6X-RAY DIFFRACTION1allD7 - 11
7X-RAY DIFFRACTION1allD13 - 24
8X-RAY DIFFRACTION1allD29 - 37
9X-RAY DIFFRACTION1allD38 - 50
10X-RAY DIFFRACTION1allD51 - 54
11X-RAY DIFFRACTION1allE1
12X-RAY DIFFRACTION1allE2 - 4

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