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- PDB-3ph2: Structure of the imidazole-adduct of the Phormidium laminosum cyt... -

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Basic information

Entry
Database: PDB / ID: 3ph2
TitleStructure of the imidazole-adduct of the Phormidium laminosum cytochrome c6 Q51V variant
ComponentsCytochrome c6
KeywordsPHOTOSYNTHESIS / Class I cytochrome c / Cytochrome f / Photosystem I / Thylakoid
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 / IMIDAZOLE / Cytochrome c6
Similarity search - Component
Biological speciesPhormidium laminosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWorrall, J.A.R.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2011
Title: Structural and kinetic studies of imidazole binding to two members of the cytochrome c (6) family reveal an important role for a conserved heme pocket residue.
Authors: Rajagopal, B.S. / Wilson, M.T. / Bendall, D.S. / Howe, C.J. / Worrall, J.A.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _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 / _pdbx_validate_close_contact.auth_comp_id_2 / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 6, 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 2.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cytochrome c6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5813
Polymers8,8931
Non-polymers6882
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.616, 45.616, 64.707
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 c6


Mass: 8893.162 Da / Num. of mol.: 1 / Mutation: Q51V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phormidium laminosum (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2Z292*PLUS
#2: Chemical ChemComp-HEC / HEME C


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


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.4 M NaH2PO4/1.6 M K2HPO4, 0.1 M imidazole ph 8.0, 0.2 M NaCl., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2006 / Details: mirrors
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→25.031 Å / Num. obs: 15086 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2V08

2v08


Resolution: 1.4→25.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22227 746 5.1 %RANDOM
Rwork0.18594 ---
obs0.18764 13988 97.67 %-
all-15086 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.884 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms589 0 48 71 708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022653
X-RAY DIFFRACTIONr_bond_other_d0.0020.02394
X-RAY DIFFRACTIONr_angle_refined_deg1.372.145897
X-RAY DIFFRACTIONr_angle_other_deg1.0283965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.647584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77625.78919
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1891591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.11151
X-RAY DIFFRACTIONr_chiral_restr0.0820.298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02118
X-RAY DIFFRACTIONr_nbd_refined0.3130.2180
X-RAY DIFFRACTIONr_nbd_other0.2040.2411
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2315
X-RAY DIFFRACTIONr_nbtor_other0.0830.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined1.0990.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.28
X-RAY DIFFRACTIONr_mcbond_it1.1861.5527
X-RAY DIFFRACTIONr_mcbond_other0.2891.5174
X-RAY DIFFRACTIONr_mcangle_it1.5432649
X-RAY DIFFRACTIONr_scbond_it2.0973292
X-RAY DIFFRACTIONr_scangle_it2.8084.5246
X-RAY DIFFRACTIONr_rigid_bond_restr1.67131284
X-RAY DIFFRACTIONr_sphericity_free3.694375
X-RAY DIFFRACTIONr_sphericity_bonded1.61331033
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 59 -
Rwork0.179 1031 -
obs--96.12 %

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