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- PDB-1ctj: CRYSTAL STRUCTURE OF CYTOCHROME C6 -

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Basic information

Entry
Database: PDB / ID: 1ctj
TitleCRYSTAL STRUCTURE OF CYTOCHROME C6
ComponentsCYTOCHROME C6
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c6
Similarity search - Component
Biological speciesMonoraphidium braunii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å
AuthorsSheldrick, G.M.
CitationJournal: Structure / Year: 1995
Title: Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin.
Authors: Frazao, C. / Soares, C.M. / Carrondo, M.A. / Pohl, E. / Dauter, Z. / Wilson, K.S. / Hervas, M. / Navarro, J.A. / De la Rosa, M.A. / Sheldrick, G.M.
History
DepositionAug 8, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / 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 / _diffrn_source.pdbx_synchrotron_site / _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_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

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Assembly

Deposited unit
A: CYTOCHROME C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9762
Polymers9,3591
Non-polymers6161
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.430, 40.430, 40.430
Angle α, β, γ (deg.)80.25, 80.25, 80.25
Int Tables number146
Space group name H-MR3
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein CYTOCHROME C6


Mass: 9359.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Monoraphidium braunii (plant) / References: UniProt: Q09099
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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 / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Msodium citrate1drop
20.025 Mglycine1drop
31.8 mMcytochrome1drop
40.375 mMtricine1drop
50.8 Msodium citrate1reservoir
60.1 Mglycine1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.80, 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: May 1, 1993
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
20.871
ReflectionResolution: 1.1→25 Å / Num. obs: 32653 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.1
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / % possible all: 93.5

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.1→25 Å / Num. parameters: 8268 / Num. restraintsaints: 10326 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.077. CHEMICALLY EQUIVALENT BONDS AND ANGLE DISTANCES IN HEME RESTRAINED TO BE EQUAL WITHOUT TARGET VALUES. NO GEOMETRIC OR ADP ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.077. CHEMICALLY EQUIVALENT BONDS AND ANGLE DISTANCES IN HEME RESTRAINED TO BE EQUAL WITHOUT TARGET VALUES. NO GEOMETRIC OR ADP RESTRAINTS APPLIED TO IRON ATOM.
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 3265 10 %EVERY 10TH REFLECTION
all0.1397 32653 --
obs0.1377 -97.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. V. 91 (1973) 201-228.
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 642 / Occupancy sum non hydrogen: 822.83
Refinement stepCycle: LAST / Resolution: 1.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 43 151 918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes0.016
X-RAY DIFFRACTIONs_zero_chiral_vol0.148
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.13
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.108

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