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- PDB-4q5p: Lysine-Ligated Yeast Iso-1 Cytochrome C -

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Basic information

Entry
Database: PDB / ID: 4q5p
TitleLysine-Ligated Yeast Iso-1 Cytochrome C
ComponentsCytochrome c iso-1
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / 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-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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsAmacher, J.F. / Zhu, M.Q. / Zhong, F. / Pletneva, E.V. / Madden, D.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch.
Authors: Amacher, J.F. / Zhong, F. / Lisi, G.P. / Zhu, M.Q. / Alden, S.L. / Hoke, K.R. / Madden, D.R. / Pletneva, E.V.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 20, 2023Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9486
Polymers35,0983
Non-polymers1,8493
Water1,54986
1
A: Cytochrome c iso-1
hetero molecules

A: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6324
Polymers23,3992
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3950 Å2
ΔGint-65 kcal/mol
Surface area10790 Å2
MethodPISA
2
B: Cytochrome c iso-1
hetero molecules

B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6324
Polymers23,3992
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area3900 Å2
ΔGint-65 kcal/mol
Surface area10690 Å2
MethodPISA
3
C: Cytochrome c iso-1
hetero molecules

C: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6324
Polymers23,3992
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3880 Å2
ΔGint-63 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.020, 106.020, 149.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Cytochrome c iso-1


Mass: 11699.359 Da / Num. of mol.: 3 / Fragment: UNP residues 7-109 / Mutation: T78C, K79G
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
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium phosphate, pH 8.1, 30% w/v PEG300, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2013
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.337
11-1/2H+1/2K-1/2L, 1/2H-1/2K-1/2L, -H-K20.311
11-1/2H-1/2K-1/2L, -1/2H-1/2K+1/2L, -H+K30.352
ReflectionResolution: 1.87→19.52 Å / Num. all: 35597 / Num. obs: 35544 / % possible obs: 99.9 % / Observed criterion σ(F): 7 / Observed criterion σ(I): 29.96 / Rmerge(I) obs: 0.072 / Rsym value: 0.07 / Net I/σ(I): 29.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.87-1.970.5974.30.567199.9
1.98-2.10.3678.471100
2.11-2.270.22613.491100
2.28-2.490.16318.211100
2.5-2.770.09529.321100
2.78-3.190.0642.881100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEA

1yea


Resolution: 1.87→19.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20367 1777 5 %RANDOM
Rwork0.17228 ---
obs0.17386 33766 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.213 Å2
Baniso -1Baniso -2Baniso -3
1--3.93 Å2-0 Å2-0 Å2
2---3.93 Å2-0 Å2
3---7.85 Å2
Refinement stepCycle: LAST / Resolution: 1.87→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 129 86 2638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192625
X-RAY DIFFRACTIONr_bond_other_d00.022455
X-RAY DIFFRACTIONr_angle_refined_deg1.2282.0313564
X-RAY DIFFRACTIONr_angle_other_deg3.54835664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3295311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5224.528106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.0715449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.514159
X-RAY DIFFRACTIONr_chiral_restr0.1550.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.023012
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02625
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1222.6111253
X-RAY DIFFRACTIONr_mcbond_other4.1072.6091252
X-RAY DIFFRACTIONr_mcangle_it5.0653.8951561
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4912.8621369
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.869→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 91 -
Rwork0.226 2451 -
obs--99.06 %

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