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- PDB-1c6o: CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GREEN ALGAE ... -

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Basic information

Entry
Database: PDB / ID: 1c6o
TitleCRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GREEN ALGAE SCENEDESMUS OBLIQUUS
ComponentsCYTOCHROME C6
KeywordsELECTRON TRANSPORT / ELECTRON TRANSPORT PROTEIN / CYTOCHROME-C6 / OXIDIZED STATE / PHOTOSYNTHESIS / DIMERIZATION
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 speciesScenedesmus obliquus (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchnackenberg, J. / Than, M.E. / Mann, K. / Wiegand, G. / Huber, R. / Reuter, W.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Amino acid sequence, crystallization and structure determination of reduced and oxidized cytochrome c6 from the green alga Scenedesmus obliquus.
Authors: Schnackenberg, J. / Than, M.E. / Mann, K. / Wiegand, G. / Huber, R. / Reuter, W.
History
DepositionApr 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C6
B: CYTOCHROME C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0644
Polymers18,8312
Non-polymers1,2332
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.560, 49.560, 152.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CYTOCHROME C6


Mass: 9415.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GENE IS NUCLEAR PETJ / Source: (natural) Scenedesmus obliquus (plant) / Cellular location: THYLAKOID LUMEN OF CHLOROPLAST / Organelle: CHLOROPLAST / Strain: D3 / References: UniProt: P57736
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1drop
22.0 Mammonium dihydrogenphosphate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 14441 / % possible obs: 98.7 % / Redundancy: 5 % / Biso Wilson estimate: 39.6 Å2 / Rsym value: 6.6 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 34.4 / % possible all: 92.4
Reflection
*PLUS
Num. measured all: 75095 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.342

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C6R

1c6r


Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
Details: OCCUPANCY AND B-FACTOR ARE SET TO ZERO FOR ALL ATOMS THAT ARE NOT DEFINED IN THE FINAL 2FO-FC ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1425 9.43 %RANDOM
Rwork0.2127 ---
obs-14435 95.48 %-
Displacement parametersBiso mean: 32.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 86 96 1504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.897
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.18
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.856
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
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4173 57 7.71 %
Rwork0.3751 552 -
obs--82.41 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 9.43 % / Rfactor obs: 0.2175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.18
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.856
LS refinement shell
*PLUS
Num. reflection obs: 552 / Rfactor obs: 0.3751

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