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- PDB-1cpr: ST. LOUIS CYTOCHROME C' FROM THE PURPLE PHOTOTROPIC BACTERIUM, RH... -

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Basic information

Entry
Database: PDB / ID: 1cpr
TitleST. LOUIS CYTOCHROME C' FROM THE PURPLE PHOTOTROPIC BACTERIUM, RHODOBACTER CAPSULATUS
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / HEME PROTEIN / CYTOCHROME
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c'
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsTahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Yasuoka, N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of cytochrome c' from Rhodobacter capsulatus strain St Louis: an unusual molecular association induced by bridging Zn ions.
Authors: Tahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: High-Resolution Crystal Structures of Two Polymorphs of Cytochrome C' from the Purple Phototrophic Bacterium Rhodobacter Capsulatus
Authors: Tahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N.
#2: Journal: Nat.Struct.Biol. / Year: 1996
Title: Concerted Movement of Side Chains in the Haem Vicinity Observed on Ligand Binding in Cytochrome C' from Rhodobacter Capsulatus
Authors: Tahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N.
History
DepositionApr 9, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _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)14,1508
Polymers13,1411
Non-polymers1,0097
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.680, 46.850, 40.750
Angle α, β, γ (deg.)90.00, 110.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYTOCHROME C'


Mass: 13140.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / Strain: ST. LOUIS / References: UniProt: P00147
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#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.: 47 / 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: 2.69 Å3/Da / Density % sol: 51 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
218 %PEG80001reservoir
30.2 Mzinc acetate1reservoir
40.1 Msodium cacodylate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 19, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 6988 / % possible obs: 85.2 % / Observed criterion σ(I): -3 / Redundancy: 3.88 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. measured all: 27125
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % possible obs: 66.4 % / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR2.1model building
X-PLOR2.1refinement
X-PLOR2.1phasing
RefinementResolution: 2.1→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.184 -
obs0.184 6440
Displacement parametersBiso mean: 21.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 43 53 1015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.02
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51

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