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- PDB-5cxm: Crystal structure of the cyanobacterial plasma membrane Rieske pr... -

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Basic information

Entry
Database: PDB / ID: 5cxm
TitleCrystal structure of the cyanobacterial plasma membrane Rieske protein PetC3 from Synechocystis PCC 6803
ComponentsCytochrome b6/f complex iron-sulfur subunit
KeywordsMETAL BINDING PROTEIN / PetC3 / sll1182 / Rieske protein / 2Fe-2S cluster / oxidoreductase / electron transport / plasma membrane / lipoprotein / cyanobacteria / Synechocystis PCC 6803
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
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] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / NICKEL (II) ION / Cytochrome b6/f complex iron-sulfur subunit
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVeit, S. / Takeda, K. / Miki, K. / Roegner, M.
CitationJournal: Biochim. Biophys. Acta / Year: 2016
Title: Structural and functional characterisation of the cyanobacterial PetC3 Rieske protein family.
Authors: Veit, S. / Takeda, K. / Tsunoyama, Y. / Baymann, F. / Nevo, R. / Reich, Z. / Rogner, M. / Miki, K. / Rexroth, S.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 8, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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
Revision 1.5Oct 30, 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 b6/f complex iron-sulfur subunit
B: Cytochrome b6/f complex iron-sulfur subunit
C: Cytochrome b6/f complex iron-sulfur subunit
D: Cytochrome b6/f complex iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,91713
Polymers44,8834
Non-polymers1,0349
Water5,242291
1
A: Cytochrome b6/f complex iron-sulfur subunit
B: Cytochrome b6/f complex iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9106
Polymers22,4412
Non-polymers4694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-66 kcal/mol
Surface area10200 Å2
MethodPISA
2
C: Cytochrome b6/f complex iron-sulfur subunit
D: Cytochrome b6/f complex iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0067
Polymers22,4412
Non-polymers5655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-55 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)21.747, 55.011, 80.709
Angle α, β, γ (deg.)80.44, 89.87, 84.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome b6/f complex iron-sulfur subunit / Rieske iron-sulfur protein


Mass: 11220.691 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 24-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: petC / Plasmid: pASK-IBA37 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P74174
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 291 / 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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 41.7 % / Description: plate-like
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 9mM NiSOx6H2O, 90mM Tris 22.5% (w/v) PEG-MME 2K, 10mM spermidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 38205 / % possible obs: 94.8 % / Redundancy: 2 % / Biso Wilson estimate: 13.8 Å2 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.5 / % possible all: 61.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+74 / Resolution: 1.7→26.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 908155.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1894 5 %RANDOM
Rwork0.185 ---
obs0.185 38191 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.3125 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å2-0.62 Å20.25 Å2
2--1.43 Å2-1.13 Å2
3----2.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: 1 / Resolution: 1.7→26.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 16 291 307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 267 5.2 %
Rwork0.245 4909 -
obs--76.6 %
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
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5so4.paramso4.top

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