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- PDB-1bbh: ATOMIC STRUCTURE OF A CYTOCHROME C' WITH AN UNUSUAL LIGAND-CONTRO... -

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Basic information

Entry
Database: PDB / ID: 1bbh
TitleATOMIC STRUCTURE OF A CYTOCHROME C' WITH AN UNUSUAL LIGAND-CONTROLLED DIMER DISSOCIATION AT 1.8 ANGSTROMS RESOLUTION
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT(HEME PROTEIN)
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsRen, Z. / Mcree, D.E.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Atomic structure of a cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 A resolution.
Authors: Ren, Z. / Meyer, T. / McRee, D.E.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Characterization of Chromatium Vinosum Cytochrome C'
Authors: Mcree, D.E. / Redford, S.M. / Meyer, T.E. / Cusanovich, M.A.
History
DepositionMay 18, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 23, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C'
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8504
Polymers27,6132
Non-polymers1,2372
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-57 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.200, 56.700, 98.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C'


Mass: 13806.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / References: UniProt: P00154
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein solution1drop
20.05 MTris-HCl1drop
30.02 %(w/v)1dropNaN3
425 %(w/v)PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 3.3 Å / Num. all: 26336 / Num. obs: 25244 / % possible obs: 96 % / Num. measured all: 102043 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 95 % / Mean I/σ(I) obs: 28.8 / Num. possible: 4304 / Num. unique obs: 4102 / Num. measured obs: 14700 / Rmerge(I) obs: 0.29

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.185 -
obs0.185 21287
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 86 221 2241
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 5 Å / Num. reflection obs: 21287 / σ(F): 2 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Total num. of bins used: 8 / Num. reflection obs: 1798 / Rfactor obs: 0.301

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