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- PDB-4eic: Crystal structure of reduced cytochrome c6 from Synechococcus sp.... -

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Basic information

Entry
Database: PDB / ID: 4eic
TitleCrystal structure of reduced cytochrome c6 from Synechococcus sp. PCC 7002 at ultra-high resolution
ComponentsCytochrome c6
KeywordsELECTRON TRANSPORT / Cytochrome C6
Function / homology
Function and homology information


plasma membrane-derived 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
HEME C / Cytochrome c6
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 Å
AuthorsKrzywda, S. / Bialek, W. / Jaskolski, M. / Szczepaniak, A.
Citation
Journal: To be Published
Title: Cytochrome c6 and c6C from Synechococcus sp. PCC 7002 - structure and function.
Authors: Bialek, W. / Krzywda, S. / Zatwarnicki, P. / Jaskolski, M. / Szczepaniak, A.
#1: Journal: Febs J. / Year: 2009
Title: Atomic-resolution structure of reduced cyanobacterial cytochrome c6 with an unusual sequence insertion.
Authors: Bialek, W. / Krzywda, S. / Jaskolski, M. / Szczepaniak, A.
#2: Journal: Biochemistry / Year: 2008
Title: Deeply branching c6-like cytochromes of cyanobacteria.
Authors: Bialek, W. / Nelson, M. / Tamiola, K. / Kallas, T. / Szczepaniak, A.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site / _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_comp_id / _struct_conn.ptnr1_auth_seq_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_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2603
Polymers9,4461
Non-polymers8142
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.86, 27.69, 44.07
Angle α, β, γ (deg.)90.0, 101.1, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c6 / Cytochrome c-553 / Cytochrome c553 / Soluble cytochrome f


Mass: 9446.432 Da / Num. of mol.: 1 / Fragment: UNP Residues 25-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: ATCC 27264 / PCC 7002 / PR-6 / Description: co-expression with pEC86 / Gene: petJ, petJ1, SYNPCC7002_A0167 / Plasmid: pUCJ1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: O30881
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.2M Ammonium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8166 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 14, 2006 / Details: mirrors
RadiationMonochromator: Ge / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8166 Å / Relative weight: 1
ReflectionResolution: 0.84→32.55 Å / Num. all: 64908 / Num. obs: 64908 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 9.45 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.21
Reflection shellResolution: 0.84→0.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.23 / Num. unique all: 4069 / % possible all: 80.6

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Processing

Software
NameClassification
AUTOMARdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DR0

3dr0


Resolution: 0.84→32.55 Å / Num. parameters: 7849 / Num. restraintsaints: 7790 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT, HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1271 974 1.5 %RANDOM
Rwork0.1056 ---
all0.1058 64908 --
obs0.1058 64908 94.8 %-
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 664.26 / Occupancy sum non hydrogen: 800.71
Refinement stepCycle: LAST / Resolution: 0.84→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 55 120 837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.057
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0039
X-RAY DIFFRACTIONs_zero_chiral_vol0.115
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.093
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.025
X-RAY DIFFRACTIONs_approx_iso_adps0.08

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