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- PDB-1ytc: THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIP... -

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Basic information

Entry
Database: PDB / ID: 1ytc
TitleTHERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIPS IN UNFOLDED PROTEINS
ComponentsYEAST ISO-2 CYTOCHROME C
KeywordsELECTRON TRANSPORT / HEME PROTEIN
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 / 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 / Cytochrome c isoform 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLuo, Y. / Brayer, G.D.
Citation
Journal: Biochemistry / Year: 1996
Title: Thermodynamic cycles as probes of structure in unfolded proteins.
Authors: McGee, W.A. / Rosell, F.I. / Liggins, J.R. / Rodriguez-Ghidarpour, S. / Luo, Y. / Chen, J. / Brayer, G.D. / Mauk, A.G. / Nall, B.T.
#1: Journal: Protein Sci. / Year: 1993
Title: The Structure and Function of Omega Loop a Replacements in Cytochrome C
Authors: Murphy, M.E.P. / Fetrow, J.S. / Burton, R.E. / Brayer, G.D.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Structure Determination and Analysis of Yeast Iso-2-Cytochrome C and a Composite Mutant Protein
Authors: Murphy, M.E.P. / Nall, B.T. / Brayer, G.D.
History
DepositionJul 3, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 2.0Mar 3, 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_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE PDB HAS GENERATED THE HELIX AND SHEET RECORDS FROM THE COORDINATES USING A PROGRAM BASED ...SHEET THE PDB HAS GENERATED THE HELIX AND SHEET RECORDS FROM THE COORDINATES USING A PROGRAM BASED ON DSSP OF W. KABSCH AND C. SANDER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YEAST ISO-2 CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1803
Polymers12,4651
Non-polymers7152
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.660, 36.660, 138.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YEAST ISO-2 CYTOCHROME C


Mass: 12465.292 Da / Num. of mol.: 1 / Mutation: N52I
Source method: isolated from a genetically manipulated source
Details: REDUCED STATE OF HEME
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P00045
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
20.1 Msodium phosphate12
30.3 M12NaCl
440 mMdithiothreitol12
590 %satammonium sulfate12

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 24, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→69.5 Å / Num. obs: 9141 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 59573 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 93.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
PROLSQrefinement
X-PLOR3.1refinement
R-AXIS(MSC)data reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.162 --
obs0.162 8985 94.8 %
Displacement parametersBiso mean: 24 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 51 116 1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.9371.5
X-RAY DIFFRACTIONx_mcangle_it2.7482.5
X-RAY DIFFRACTIONx_scbond_it3.5492
X-RAY DIFFRACTIONx_scangle_it5.3083
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d0.0220.036
X-RAY DIFFRACTIONx_planar_d0.050.054
X-RAY DIFFRACTIONx_plane_restr0.010.011
X-RAY DIFFRACTIONx_chiral_restr0.080.129

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