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- PDB-1crj: THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATE... -

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Basic information

Entry
Database: PDB / ID: 1crj
TitleTHE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT(CYTOCHROME)
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: 2.05 Å
AuthorsBerghuis, A.M. / Brayer, G.D.
Citation
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.
#1: Journal: To be Published
Title: Mutation of Tyrosine-67 in Cytochrome C Significantly Alters the Local Heme Environment
Authors: Berghuis, A.M. / Guillemette, G.J. / Smith, M. / Brayer, G.D.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Effect of the Asn 52-> Ile Mutation on the Redox Potential of Yeast Cytochrome C: Theory and Experiment
Authors: Langen, R. / Brayer, G.D. / Berghuis, A.M. / Mclendon, G. / Sherman, F. / Warshel, A.
#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.Biol.Chem. / Year: 1991
Title: Enhanced Thermodynamic Stabilities of Yeast Iso-1-Cytochrome C with Amino Acid Replacements at Position 52 and 102
Authors: Hickey, D.R. / Berghuis, A.M. / Lafond, G. / Jaeger, J.A. / Cardillo, T.S. / Mclendon, D. / Das, G. / Sherman, F. / Brayer, G.D. / Mclendon, G.
#5: Journal: Adv.Chem.Ser. / Year: 1991
Title: Effects of Reaction Free Energy in Biological Electron Transfer in Vitro and in Vivo (in: Electron Transfer in Inorganic, Organic, and Biological Systems)
Authors: Mclendon, G. / Hickey, D.R. / Berghuis, A.M. / Sherman, F. / Brayer, G.D.
#6: 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.
#7: 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
DepositionAug 6, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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
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)12,8113
Polymers12,0971
Non-polymers7152
Water93752
1
A: CYTOCHROME C
hetero molecules

A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6236
Polymers24,1942
Non-polymers1,4294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)36.560, 36.560, 137.530
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 TO THE SG ATOMS OF CYS 14 AND CYS 17.

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Components

#1: Protein CYTOCHROME C /


Mass: 12096.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POTENTIAL / 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.: 52 / 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 ...THIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO A THREONINE RESIDUE. IN TURN T5 THE H-BOND IS MEDIATED THROUGH A WATER MOLECULE.

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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: 35.45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: using a hair-seeding / PH range low: 6.4 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium phosphate1reservoir
286-94 %satammonium sulphate1reservoir
320 mMDTT1dropcan be replaced with 70mM sodium dithionite

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.05 Å / Num. obs: 5700 / Num. measured all: 33491 / Rmerge(I) obs: 0.07

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.179 / Highest resolution: 2.05 Å
Refinement stepCycle: LAST / Highest resolution: 2.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 0 51 52 950
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.05 Å / Num. reflection obs: 5406 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.044
X-RAY DIFFRACTIONp_plane_restr0.017
X-RAY DIFFRACTIONp_chiral_restr0.215

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