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- PDB-4eid: Crystal structure of cytochrome c6 Q57V mutant from Synechococcus... -

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Basic information

Entry
Database: PDB / ID: 4eid
TitleCrystal structure of cytochrome c6 Q57V mutant from Synechococcus sp. PCC 7002
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: 1.13 Å
AuthorsKrzywda, S. / Bialek, W. / Zatwarnicki, P. / 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 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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_ref_seq_dif.details / _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
Revision 2.2Oct 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 c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2313
Polymers9,4171
Non-polymers8142
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.781, 27.637, 44.099
Angle α, β, γ (deg.)90.0, 101.16, 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: 9417.434 Da / Num. of mol.: 1 / Fragment: UNP Residues 25-117 / Mutation: Q57V
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


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


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


Mass: 18.015 Da / Num. of mol.: 140 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.03 %
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: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 13, 2010 / 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: 1.13→50 Å / Num. all: 28144 / Num. obs: 28144 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2 / Num. unique all: 4430 / % possible all: 96.8

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Processing

Software
NameVersionClassification
AUTOMARdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DR0

3dr0


Resolution: 1.13→43.26 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.177 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17574 986 3.5 %RANDOM
Rwork0.13797 ---
all0.13931 27159 --
obs0.13931 27159 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.85 Å2
2--0.08 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.13→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms660 0 55 140 855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022755
X-RAY DIFFRACTIONr_bond_other_d0.0020.02457
X-RAY DIFFRACTIONr_angle_refined_deg1.8722.1311037
X-RAY DIFFRACTIONr_angle_other_deg1.2443.0041122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.598596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81626.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1415102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.177151
X-RAY DIFFRACTIONr_chiral_restr0.1270.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02867
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02130
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.81.5465
X-RAY DIFFRACTIONr_mcbond_other0.8721.5195
X-RAY DIFFRACTIONr_mcangle_it2.3642727
X-RAY DIFFRACTIONr_scbond_it3.3563290
X-RAY DIFFRACTIONr_scangle_it4.2724.5309
X-RAY DIFFRACTIONr_rigid_bond_restr1.52831212
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.13→1.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 71 -
Rwork0.292 1941 -
obs--100 %

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