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- PDB-1f1c: CRYSTAL STRUCTURE OF CYTOCHROME C549 -

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Basic information

Entry
Database: PDB / ID: 1f1c
TitleCRYSTAL STRUCTURE OF CYTOCHROME C549
ComponentsCYTOCHROME C549
KeywordsELECTRON TRANSPORT / dimeric cytochrome
Function / homology
Function and homology information


cytochrome c-heme linkage / thylakoid membrane / photosystem II / photosynthesis, light reaction / respiratory electron transport chain / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / 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 c-550
Similarity search - Component
Biological speciesArthrospira maxima (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKerfeld, C.A. / Sawaya, M.R. / Yeates, T.O. / Krogmann, D.W.
Citation
Journal: Biochemistry / Year: 2001
Title: Structures of cytochrome c-549 and cytochrome c6 from the cyanobacterium Arthrospira maxima.
Authors: Sawaya, M.R. / Krogmann, D.W. / Serag, A. / Ho, K.K. / Yeates, T.O. / Kerfeld, C.A.
#1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1991
Title: The Low-Potential Cytochrome C of Cyanobacteria and Algae
Authors: Krogmann, D.W.
#2: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1984
Title: Characterization of Cytochrome c-550 from Cyanobacteria
Authors: Alam, J. / Sprinkle, J. / Hermodson, M.A. / Krogmann, D.W.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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 / _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_auth_seq_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_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_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.ptnr2_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C549
B: CYTOCHROME C549
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6614
Polymers28,4242
Non-polymers1,2372
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-67 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.500, 84.400, 43.800
Angle α, β, γ (deg.)90.00, 96.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYTOCHROME C549


Mass: 14212.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arthrospira maxima (bacteria) / References: UniProt: P82603
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 0.4M ammonium acetate, pH 4.5, VAPOR DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111.7 mg/mlprotein1drop
20.4 Mammonium acetate1reservoir
35 %MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 12, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→500 Å / Num. all: 8556 / Num. obs: 8556 / % possible obs: 73.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.24
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.19 / % possible all: 60
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 60 %

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 866 random
Rwork0.217 --
all0.237 8556 -
obs0.237 8556 -
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 86 17 2103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_bond_d0.008
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.008

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