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- PDB-6tsy: Cytochrome c6 from Thermosynechococcus elongatus in a monoclinic ... -

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Basic information

Entry
Database: PDB / ID: 6tsy
TitleCytochrome c6 from Thermosynechococcus elongatus in a monoclinic space group
ComponentsCytochrome c6
KeywordsPHOTOSYNTHESIS / Cyanobacteria / heme / electron transport / photosystem I
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 speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFeiler, C.G. / Falke, S. / Sarrou, I.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structures of native cytochrome c6from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization.
Authors: Falke, S. / Feiler, C. / Chapman, H. / Sarrou, I.
History
DepositionDec 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id
Revision 1.2Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c6
B: Cytochrome c6
C: Cytochrome c6
D: Cytochrome c6
E: Cytochrome c6
F: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,93113
Polymers55,1246
Non-polymers3,8077
Water3,189177
1
A: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8062
Polymers9,1871
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8062
Polymers9,1871
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8062
Polymers9,1871
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8062
Polymers9,1871
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9023
Polymers9,1871
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8062
Polymers9,1871
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.019, 109.905, 55.402
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-328-

HOH

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Components

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


Mass: 9187.367 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A3X9
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.87 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2M ammonium sulfate, 40mM KNO3 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→41.76 Å / Num. obs: 28317 / % possible obs: 95.51 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.84 Å2 / CC1/2: 0.92 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.1 / Rrim(I) all: 0.19 / Net I/σ(I): 9.93
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.57 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2409 / CC1/2: 0.466 / Rpim(I) all: 1.01 / Rrim(I) all: 1.88 / % possible all: 80.72

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIC

4eic


Resolution: 2.25→41.76 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.6
RfactorNum. reflection% reflection
Rfree0.2512 1415 5 %
Rwork0.1878 --
obs0.191 28283 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 263 177 4257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144195
X-RAY DIFFRACTIONf_angle_d1.2695738
X-RAY DIFFRACTIONf_dihedral_angle_d19.345586
X-RAY DIFFRACTIONf_chiral_restr0.064558
X-RAY DIFFRACTIONf_plane_restr0.007735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.330.44061190.41612274X-RAY DIFFRACTION81
2.33-2.420.32521430.29732716X-RAY DIFFRACTION98
2.42-2.530.34261450.27022742X-RAY DIFFRACTION98
2.53-2.670.36781420.27272693X-RAY DIFFRACTION96
2.67-2.830.30961420.21712705X-RAY DIFFRACTION97
2.83-3.050.26891470.21392801X-RAY DIFFRACTION99
3.05-3.360.25851450.17432746X-RAY DIFFRACTION99
3.36-3.850.24111390.16442647X-RAY DIFFRACTION93
3.85-4.850.17891440.12392717X-RAY DIFFRACTION97
4.85-41.760.18271490.13552827X-RAY DIFFRACTION99

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