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- PDB-1csv: REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HE... -

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Basic information

Entry
Database: PDB / ID: 1csv
TitleREPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT(HEME PROTEIN)
Function / homology
Function and homology information


Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / 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: 1.9 Å
AuthorsLo, T.P. / Brayer, G.D.
Citation
Journal: Protein Sci. / Year: 1995
Title: Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c.
Authors: Lo, T.P. / Murphy, M.E. / Guillemette, J.G. / Smith, M. / Brayer, G.D.
#1: Journal: Biochemistry / Year: 1995
Title: Structural Studies of the Roles of Residues 82 and 85 at the Interactive Face of Cytochrome C
Authors: Lo, T.P. / Guillemette, J.G. / Louie, G.V. / Smith, M. / Brayer, G.D.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Oxidation State-Dependent Conformational Changes in Cytochrome C
Authors: Berghuis, A.M. / Brayer, G.D.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#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.
History
DepositionOct 4, 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 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / 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_database_status.process_site / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8623
Polymers12,1481
Non-polymers7152
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.550, 36.550, 138.240
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: 12147.893 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 / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO A THREONINE RESIDUE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein1drop
275 %satammonium sulfate1drop
30.1 Msodium phosphate1drop
490 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 8072

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.192 4466 57.2 %
Displacement parametersBiso mean: 16.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms854 0 48 58 960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4531.5
X-RAY DIFFRACTIONp_mcangle_it2.1062
X-RAY DIFFRACTIONp_scbond_it3.0142.5
X-RAY DIFFRACTIONp_scangle_it4.1683.5
X-RAY DIFFRACTIONp_plane_restr0.0130.018
X-RAY DIFFRACTIONp_chiral_restr0.160.12
X-RAY DIFFRACTIONp_singtor_nbd0.2150.25
X-RAY DIFFRACTIONp_multtor_nbd0.2020.25
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.25
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.92.5
X-RAY DIFFRACTIONp_staggered_tor22.920
X-RAY DIFFRACTIONp_orthonormal_tor2215
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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