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- PDB-1irv: CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY M... -

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Basic information

Entry
Database: PDB / ID: 1irv
TitleCYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY MET AND CYS 102 REPLACED BY THR
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT / HEME PROTEIN / MITOCHONDRION
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-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 / Resolution: 1.9 Å
AuthorsBerghuis, A.M. / Brayer, G.D.
Citation
Journal: Biochemistry / Year: 1996
Title: Mechanistic and structural contributions of critical surface and internal residues to cytochrome c electron transfer reactivity.
Authors: Rafferty, S.P. / Guillemette, J.G. / Berghuis, A.M. / Smith, M. / Brayer, G.D. / Mauk, A.G.
#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. / Smith, M. / 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: Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique
Authors: Leung, C.J. / Nall, B.T. / Brayer, G.D.
History
DepositionJun 27, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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.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.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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8443
Polymers12,1321
Non-polymers7132
Water52229
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, 138.590
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 CYTOCHROME C


Mass: 12131.914 Da / Num. of mol.: 1 / Mutation: I75M, C102T
Source method: isolated from a genetically manipulated source
Details: ISOZYME 1, REDUCED
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 35.5 %
Crystal grow
*PLUS
pH: 5.3 / Method: unknown / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium phosphate11
295 %satammonium sulfate11
370 mMsodium dithionite11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→6 Å / Num. obs: 8110 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 1 %

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Processing

Software
NameVersionClassification
PROLSQrefinement
IN-HOUSESOFTWAREdata reduction
RefinementResolution: 1.9→6 Å / σ(F): 2
Details: PROLSQ STANDARD SET OF IDEAL BOND LENGTHS ETC. (I.E. VERY SIMILAR TO ENGH & HUBER) ESTIMATED COORD. ERROR 0.25 ANGSTROMS FINAL RMS COORD. SHIFT 0.35 ANGSTROMS
RfactorNum. reflection% reflection
Rwork0.222 --
obs-3645 100 %
Displacement parametersBiso mean: 18.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 48 29 928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.050.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0640.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.941.5
X-RAY DIFFRACTIONp_mcangle_it2.9892.5
X-RAY DIFFRACTIONp_scbond_it2.6662
X-RAY DIFFRACTIONp_scangle_it4.1183
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.2860.16
X-RAY DIFFRACTIONp_singtor_nbd0.2360.25
X-RAY DIFFRACTIONp_multtor_nbd0.2420.25
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2620.25
X-RAY DIFFRACTIONp_planar_tor2.62.5
X-RAY DIFFRACTIONp_staggered_tor26.312
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.615
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS

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