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- PDB-1c2r: MOLECULAR STRUCTURE OF CYTOCHROME C2 ISOLATED FROM RHODOBACTER CA... -

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Basic information

Entry
Database: PDB / ID: 1c2r
TitleMOLECULAR STRUCTURE OF CYTOCHROME C2 ISOLATED FROM RHODOBACTER CAPSULATUS DETERMINED AT 2.5 ANGSTROMS RESOLUTION
ComponentsCYTOCHROME C2
KeywordsELECTRON TRANSPORT PROTEIN (CYTOCHROME)
Function / homology
Function and homology information


photosynthesis / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / 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 c2
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBenning, M.M. / Wesenberg, G. / Caffrey, M.S. / Bartsch, R.G. / Meyer, T.E. / Cusanovich, M.A. / Rayment, I. / Holden, H.M.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: Molecular structure of cytochrome c2 isolated from Rhodobacter capsulatus determined at 2.5 A resolution.
Authors: Benning, M.M. / Wesenberg, G. / Caffrey, M.S. / Bartsch, R.G. / Meyer, T.E. / Cusanovich, M.A. / Rayment, I. / Holden, H.M.
History
DepositionMar 19, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: 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 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 / database_PDB_caveat / 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_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_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 C2
B: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8094
Polymers24,5722
Non-polymers1,2372
Water1,65792
1
A: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9052
Polymers12,2861
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9052
Polymers12,2861
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.030, 100.030, 162.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein CYTOCHROME C2


Mass: 12286.013 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / References: UniProt: P00094
#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.2-3.5 Mammonium sulfate1reservoir
2250 mM1reservoirNaCl
350 mMsodium potassium phosphate1reservoir
410-30 mg/mlprotein1drop
510 mMsodium potassium phospahte1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 9496 / Num. measured all: 12788 / Rmerge(I) obs: 0.039

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.168 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 86 92 1906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.635
X-RAY DIFFRACTIONt_dihedral_angle_d17.588
X-RAY DIFFRACTIONt_trig_c_planes0.01
X-RAY DIFFRACTIONt_gen_planes0.007
Refinement
*PLUS
Lowest resolution: 100 Å / Num. reflection obs: 9496
Solvent computation
*PLUS
Displacement parameters
*PLUS

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