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- PDB-6tr1: Native cytochrome c6 from Thermosynechococcus elongatus in space ... -

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Basic information

Entry
Database: PDB / ID: 6tr1
TitleNative cytochrome c6 from Thermosynechococcus elongatus in space group H3
Components(Cytochrome c6) x 3
KeywordsPHOTOSYNTHESIS / Photosystem I / Heme / Cyanobacteria / Electron transport
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFalke, S. / Feiler, C.G. / 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 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
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_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
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c6
C: Cytochrome c6
E: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,51611
Polymers27,5453
Non-polymers1,9708
Water99155
1
A: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8143
Polymers9,1721
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9256
Polymers9,2141
Non-polymers7105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7772
Polymers9,1581
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.800, 94.800, 160.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 3 types, 3 molecules ACE

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


Mass: 9172.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
References: UniProt: P0A3X9
#2: Protein Cytochrome c6 / Cytochrome c-553 / Cytochrome c553 / Soluble cytochrome f


Mass: 9214.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
References: UniProt: P0A3X9
#3: Protein Cytochrome c6 / Cytochrome c-553 / Cytochrome c553 / Soluble cytochrome f


Mass: 9158.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Cytochrome c6
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
References: UniProt: P0A3X9

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Non-polymers , 3 types, 63 molecules

#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 6.5 / Details: Ammonium sulfate, potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.522
11K, H, -L20.478
ReflectionResolution: 1.189→73.065 Å / Num. all: 170023 / Num. obs: 170023 / % possible obs: 98.5 % / Redundancy: 3.1 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.12 / Rsym value: 0.101 / Net I/av σ(I): 4.5 / Net I/σ(I): 4.7 / Num. measured all: 524507
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.19-1.253.11.5550.576258249511.0261.8731.5550.898.7
1.25-1.332.91.4510.566753233200.9921.7681.4510.898
1.33-1.423.11.3030.670005222550.851.5631.3030.999.2
1.42-1.542.90.9020.859005205020.6161.0980.9021.298.1
1.54-1.683.20.5761.361371189940.370.6880.5762.198.9
1.68-1.8830.2812.751414171230.1860.3390.2813.998.7
1.88-2.173.30.1216.249937152110.0770.1430.1218.699.3
2.17-2.663.10.0848.338999126320.0550.1010.08413.397.6
2.66-3.763.40.05211.83327197480.0320.0610.05219.397.7
3.76-36.5333.30.04413.71749452870.0270.0520.04421.896.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIC

4eic


Resolution: 1.7→36.53 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.1862 / FOM work R set: 0.8697 / SU B: 1.005 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0146 / SU Rfree: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.015 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 2864 4.9 %RANDOM
Rwork0.1857 ---
obs0.1868 55146 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.4 Å2 / Biso mean: 21.067 Å2 / Biso min: 10.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.3 Å20 Å20 Å2
2--3.3 Å20 Å2
3----6.59 Å2
Refinement stepCycle: final / Resolution: 1.7→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 134 55 2111
Biso mean--15.59 25.23 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0192108
X-RAY DIFFRACTIONr_bond_other_d0.0020.021953
X-RAY DIFFRACTIONr_angle_refined_deg2.8042.0212882
X-RAY DIFFRACTIONr_angle_other_deg1.28134455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69826.29289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50315324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.86153
X-RAY DIFFRACTIONr_chiral_restr0.2070.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.020.022517
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02516
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 207 -
Rwork0.201 4100 -
all-4307 -
obs--98.99 %

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