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- PDB-4eif: Crystal structure of cytochrome c6C L50Q mutant from Synechococcu... -

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Basic information

Entry
Database: PDB / ID: 4eif
TitleCrystal structure of cytochrome c6C L50Q mutant from Synechococcus sp. PCC 7002
ComponentsCytochrome c6
KeywordsELECTRON TRANSPORT / cytochrome c6C
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 / molecular replacement / Resolution: 1.04 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: 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 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_asym_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_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)10,2579
Polymers9,4271
Non-polymers8298
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)56.38, 56.38, 50.05
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-106-

CL

21A-238-

HOH

31A-281-

HOH

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Components

#1: Protein Cytochrome c6 / Putative cytochrome c6-2


Mass: 9427.482 Da / Num. of mol.: 1 / Fragment: UNP Residues 29-115 / Mutation: L50Q
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, petJ2, SYNPCC7002_A2391 / Plasmid: pUCPF2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q8KX15
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 15 mg/ml cytochrome c6C in 0.1 M TRIS pH 7.5, 0.2 M NaCl and 1 mM PMSF; Precipitant solution: 2 M NaCl and 2 M NH4)2SO4., VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 5, 2011 / Details: mirrors
RadiationMonochromator: Triangular Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.04→31.18 Å / Num. all: 39071 / Num. obs: 39071 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 10.127 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.25
Reflection shellResolution: 1.04→1.1 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 7.8 / Num. measured obs: 44534 / Num. unique all: 5898 / Num. unique obs: 5898 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å31.18 Å
Translation3.5 Å31.18 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EIE

4eie


Resolution: 1.04→31.18 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.133 / WRfactor Rwork: 0.109 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.518 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.023 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1449 977 2.5 %RANDOM
Rwork0.1191 ---
all0.1197 39071 --
obs0.1197 39071 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 44.28 Å2 / Biso mean: 10.5564 Å2 / Biso min: 3.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.04→31.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 50 140 812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022735
X-RAY DIFFRACTIONr_bond_other_d0.0030.02497
X-RAY DIFFRACTIONr_angle_refined_deg1.8552.1061000
X-RAY DIFFRACTIONr_angle_other_deg1.3973.0031209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.941587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61125.27836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34615134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.01155
X-RAY DIFFRACTIONr_chiral_restr0.1360.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02823
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02134
X-RAY DIFFRACTIONr_mcbond_it1.7451.5426
X-RAY DIFFRACTIONr_mcbond_other0.5841.5182
X-RAY DIFFRACTIONr_mcangle_it2.522674
X-RAY DIFFRACTIONr_scbond_it3.2693309
X-RAY DIFFRACTIONr_scangle_it4.4664.5324
X-RAY DIFFRACTIONr_rigid_bond_restr1.2531232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.04-1.0670.201700.16527282798
1.067-1.0960.166690.12526952764
1.096-1.1280.097680.09526542722
1.128-1.1630.142660.09925672633
1.163-1.2010.12630.09124752538
1.201-1.2430.115620.08923952457
1.243-1.290.124590.08923322391
1.29-1.3420.13580.09222442302
1.342-1.4020.125550.09121402195
1.402-1.470.143520.09520432095
1.47-1.5490.099500.0919431993
1.549-1.6430.14470.09918431890
1.643-1.7560.126450.10817521797
1.756-1.8970.143420.11516401682
1.897-2.0770.132390.11215311570
2.077-2.3210.092360.12713991435
2.321-2.6770.164330.13812551288
2.677-3.2730.218270.15410701097
3.273-4.6030.174220.142857879
4.603-31.1830.198140.208531545

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