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- PDB-1cih: STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL... -

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Basic information

Entry
Database: PDB / ID: 1cih
TitleSTRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C
ComponentsCYTOCHROME 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 / 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
HEME C / Cytochrome c isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLo, T.P. / Brayer, G.D.
Citation
Journal: Biochemistry / Year: 1995
Title: Structural and functional effects of multiple mutations at distal sites in cytochrome c.
Authors: Lo, T.P. / Komar-Panicucci, S. / Sherman, F. / McLendon, G. / Brayer, G.D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: The Role of a Conserved Internal Water Molecule and its Associated Hydrogen Bond Network in Cytochrome C
Authors: Berghuis, A.M. / Guillemette, J.G. / Mclendon, G. / Sherman, F. / Brayer, G.D.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Mutation of Tyrosine-67 to Phenylalanine in Cytochrome C Significantly Alters the Local Heme Environment
Authors: Berghuis, A.M. / Guillemette, J.G. / Smith, M. / Brayer, G.D.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Oxidation State-Dependent Conformational Changes in Cytochrome C
Authors: Berghuis, A.M. / Brayer, G.D.
#4: Journal: J.Mol.Biol. / Year: 1990
Title: High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C
Authors: Louie, G.V. / Brayer, G.D.
#5: Journal: J.Mol.Biol. / Year: 1989
Title: A Polypeptide Chain-Refolding Event Occurs in the Gly82 Variant of Yeast Iso-1-Cytochrome C
Authors: Louie, G.V. / Brayer, G.D.
#6: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique
Authors: Leung, C.J. / Nall, B.T. / Brayer, G.D.
#7: Journal: Biochemistry / Year: 1988
Title: Role of Phenylalanine-82 in Yeast Iso-1-Cytochrome C and Remote Conformational Changes Induced by a Serine Residue at This Position
Authors: Louie, G.V. / Pielak, G.J. / Smith, M. / Brayer, G.D.
#8: Journal: J.Mol.Biol. / Year: 1988
Title: Yeast Iso-1-Cytochrome C. A 2.8 Angstrom Resolution Three-Dimensional Structure Determination
Authors: Louie, G.V. / Hutcheon, W.L.B. / Brayer, G.D.
History
DepositionSep 26, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650HELIX THE END OF THE 50 HELIX (RESIDUE 55) IS DISTORTED.
Remark 700SHEET RESIDUES IN SHEET S1 FORM A HIGHLY DISTORTED BETA TYPE CONFORMATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6513
Polymers11,9371
Non-polymers7152
Water1,20767
1
A: CYTOCHROME C
hetero molecules

A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3036
Polymers23,8732
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)36.480, 36.480, 137.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: THE HEME GROUP IS COVALENTLY ATTACHED TO THE PROTEIN VIA THIOETHER BONDS FROM THE SG ATOMS OF CYS 14 AND CYS 17, TO THE CAB AND CAC HEME ATOMS, RESPECTIVELY.
2: RESIDUE 72 IS EPSILON-N-TRIMETHYLLYSINE. THE THREE METHYL CARBONS FOR THIS RESIDUE ARE PRESENT AS HETATMS WITH RESIDUE NAME TML (FOLLOWING THE HEME). RESIDUE 72 IS IDENTIFIED AS LYS ON THE ATOM ...2: RESIDUE 72 IS EPSILON-N-TRIMETHYLLYSINE. THE THREE METHYL CARBONS FOR THIS RESIDUE ARE PRESENT AS HETATMS WITH RESIDUE NAME TML (FOLLOWING THE HEME). RESIDUE 72 IS IDENTIFIED AS LYS ON THE ATOM AND SEQRES RECORDS. RESIDUE LYS 72 IS TRIMETHYLATED AT THE AMINO END OF ITS SIDE CHAIN.
3: RESIDUES MET 80 AND HIS 18 FORM HEME IRON LIGAND BONDS.

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Components

#1: Protein CYTOCHROME C


Mass: 11936.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00044
#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.: 67 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO AN ALANINE RESIDUE. ...THIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO AN ALANINE RESIDUE. IN TURN T5 THE H-BOND IS MEDIATED THROUGH A WATER MOLECULE.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.91 %
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
175 %satammonium sulfate1drop
22 mg/mlcytochrome c1drop
30.1 Msodium phosphate1drop
490 %satammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 8999 / Num. measured all: 71744 / Rmerge(I) obs: 0.064

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.2 8587
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 51 67 953
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0390.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5021.5
X-RAY DIFFRACTIONp_mcangle_it2.1362
X-RAY DIFFRACTIONp_scbond_it3.32.5
X-RAY DIFFRACTIONp_scangle_it4.7593.5
X-RAY DIFFRACTIONp_plane_restr0.0140.018
X-RAY DIFFRACTIONp_chiral_restr0.1560.12
X-RAY DIFFRACTIONp_singtor_nbd0.2110.25
X-RAY DIFFRACTIONp_multtor_nbd0.1930.25
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1830.25
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.52.5
X-RAY DIFFRACTIONp_staggered_tor18.520
X-RAY DIFFRACTIONp_orthonormal_tor2515
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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