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- PDB-2ccy: STRUCTURE OF FERRICYTOCHROME C(PRIME) FROM RHODOSPIRILLUM MOLISCH... -

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Basic information

Entry
Database: PDB / ID: 2ccy
TitleSTRUCTURE OF FERRICYTOCHROME C(PRIME) FROM RHODOSPIRILLUM MOLISCHIANUM AT 1.67 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 speciesPhaeospirillum molischianum (magnetotactic)
MethodX-RAY DIFFRACTION / Resolution: 1.67 Å
AuthorsFinzel, B.C. / Weber, P.C. / Hardman, K.D. / Salemme, F.R.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Structure of ferricytochrome c' from Rhodospirillum molischianum at 1.67 A resolution.
Authors: Finzel, B.C. / Weber, P.C. / Hardman, K.D. / Salemme, F.R.
#1: Journal: Nature / Year: 1985
Title: Lattice Mobility and Anomalous Temperature Factor Behaviour in Cytochrome C(Prime)
Authors: Finzel, B.C. / Salemme, F.R.
#2: Journal: J.Mol.Biol. / Year: 1981
Title: Crystallographic Structure of Rhodospirillum Molischianum Ferricytochrome C(Prime) at 2.5 Angstroms Resolution
Authors: Weber, P.C. / Howard, A. / Xuong, N.H. / Salemme, F.R.
#3: Journal: Biochemistry / Year: 1982
Title: Correlations between Structural and Spectroscopic Properties of the High-Spin Heme Protein Cytochrome C(Prime)
Authors: Weber, P.C.
#4: Journal: J.Biol.Chem. / Year: 1981
Title: On the Evolutionary Relationship of the 4-Alpha-Helical Heme Proteins. The Comparison of Cytochrome B562 and Cytochrome C(Prime)
Authors: Weber, P.C. / Salemme, F.R. / Mathews, F.S. / Bethge, P.H.
#5: Journal: Nature / Year: 1980
Title: Structural and Functional Diversity in 4-Alpha-Helical Proteins
Authors: Weber, P.C. / Salemme, F.R.
#6: Journal: Nature / Year: 1980
Title: Structure of Cytochrome C(Prime). A Dimeric, High-Spin Haem Protein
Authors: Weber, P.C. / Bartsch, R.G. / Cusanovich, M.A. / Hamlin, R.C. / Howard, A. / Jordan, S.R. / Kamen, M.D. / Meyer, T.E. / Weatherford, D.W. / Xuong, N.H. / Salemme, F.R.
#7: Journal: J.Mol.Biol. / Year: 1977
Title: Preliminary Crystallographic Data for Cytochromes C(Prime) of Rhodopseudomonas Capsulata and Rhodospirillum Molischianum
Authors: Weber, P. / Salemme, F.R.
History
DepositionAug 27, 1985Processing site: BNL
SupersessionJan 21, 1986ID: 1CCY
Revision 1.0Jan 21, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 / 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 16, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,1164
Polymers26,8792
Non-polymers1,2372
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-63 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.580, 72.330, 75.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE GLN 42 IN BOTH CHAINS IS MODELLED IN TWO CONFORMATIONS.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4673, 0.2938, -0.8339), (0.3022, -0.9394, -0.1616), (-0.8309, -0.1765, -0.5277)
Vector: 14.6, 27.06, 35.31)

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Components

#1: Protein CYTOCHROME C


Mass: 13439.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeospirillum molischianum (magnetotactic)
References: UniProt: P00152
#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.: 194 / 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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Details: referred to 'Weber, P.', (1977) J.Mol.Biol., 117, 815-820
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
240 %satammonium sulfate1drop
30.05 Mmagnesium nitrate1drop
4ammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.66 Å / Num. obs: 46290 / % possible obs: 72 % / Observed criterion σ(I): 1 / Num. measured all: 213471

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.67 Å / Num. reflection obs: 30533 / σ(I): 1
Refinement stepCycle: LAST / Highest resolution: 1.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 86 194 2146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.03
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
σ(I): 1 / Highest resolution: 1.67 Å / Lowest resolution: 9999 Å / Num. reflection obs: 30533 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONo_bond_d0.03
X-RAY DIFFRACTIONo_angle_d0.050.051
X-RAY DIFFRACTIONo_planar_d0.050.059
X-RAY DIFFRACTIONo_chiral_restr0.40.33
LS refinement shell
*PLUS
Lowest resolution: 9999 Å

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