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- PDB-3azc: Crystal structure of the soluble part of cytochrome b6f complex i... -

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Basic information

Entry
Database: PDB / ID: 3azc
TitleCrystal structure of the soluble part of cytochrome b6f complex iron-sulfur subunit from Thermosynechococcus elongatus BP-1
ComponentsCytochrome b6-f complex iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Rieske / cytochrome b6f complex / Thermosynechococcus elongatus / photosynthesis / electron transport / thylakoid membrane
Function / homology
Function and homology information


plastoquinol--plastocyanin reductase activity / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / thylakoid membrane / photosynthesis / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Cytochrome b6-f complex iron-sulfur subunit / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Cytochrome b6-f complex iron-sulfur subunit
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVeit, S. / Takeda, K. / Tsunoyama, Y. / Roegner, M. / Miki, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of a thermophilic cyanobacterial b(6)f-type Rieske protein
Authors: Veit, S. / Takeda, K. / Tsunoyama, Y. / Rexroth, D. / Rogner, M. / Miki, K.
History
DepositionMay 23, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_atom_id / _struct_ref_seq_dif.details / _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 b6-f complex iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8212
Polymers14,6461
Non-polymers1761
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.324, 91.324, 43.342
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cytochrome b6-f complex iron-sulfur subunit / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein / ISP / RISP / Rieske iron-sulfur protein


Mass: 14645.560 Da / Num. of mol.: 1 / Fragment: soluble domain, UNP residues 54-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: petC, tlr0959 / Plasmid: pASK-IBA37 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Competent Cells / References: UniProt: P0C8N8, EC: 1.10.99.1
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.56 Å3/Da / Density % sol: 65.47 % / Description: SF file contains friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Na-HEPES, 10% 2-propanol, 20% PEG 3000, 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 40 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.65 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 2, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 24682 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.076 / Net I/σ(I): 32.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 798 / Rsym value: 0.471 / % possible all: 57.1

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E74

2e74


Resolution: 2→24.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1510995.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 1. SF FILE CONTAINS FRIEDEL PAIRS UNDER I_PLUS/MINUS COLUMN 2. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1141 5 %RANDOM
Rwork0.197 ---
all-22697 --
obs-22697 83 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 87.6452 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 58.1 Å2
Baniso -1Baniso -2Baniso -3
1--15.84 Å20 Å20 Å2
2---15.84 Å20 Å2
3---31.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 4 98 1134
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it4.821.5
X-RAY DIFFRACTIONc_mcangle_it6.112
X-RAY DIFFRACTIONc_scbond_it6.982
X-RAY DIFFRACTIONc_scangle_it8.042.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 145 6.3 %
Rwork0.319 2166 -
obs--50.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2fes_rieske01.paramfes_rieske01.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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