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- PDB-2yk3: CRITHIDIA FASCICULATA CYTOCHROME C -

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Basic information

Entry
Database: PDB / ID: 2yk3
TitleCRITHIDIA FASCICULATA CYTOCHROME C
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT / INTERMEMBRANE SPACE / METAL-BINDING / THIOETHER BOND / RESPIRATORY CHAIN / TRYPANOSOME / MITOCHONDRION
Function / homology
Function and homology information


respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / 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
Similarity search - Component
Biological speciesCRITHIDIA FASCICULATA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFulop, V. / Sam, K.A. / Ferguson, S.J. / Ginger, M.L. / Allen, J.W.A.
CitationJournal: FEBS J. / Year: 2009
Title: Structure of a Trypanosomatid Mitochondrial Cytochrome C with Heme Attached Via Only One Thioether Bond and Implications for the Substrate Recognition Requirements of Heme Lyase.
Authors: Fulop, V. / Sam, K.A. / Ferguson, S.J. / Ginger, M.L. / Allen, J.W.A.
History
DepositionMay 25, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionJun 15, 2011ID: 2W9K
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references / Version format compliance
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / exptl_crystal_grow / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
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 / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _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.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Dec 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _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 C
B: CYTOCHROME C
C: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,05913
Polymers36,5313
Non-polymers2,52810
Water10,142563
1
A: CYTOCHROME C
B: CYTOCHROME C
C: CYTOCHROME C
hetero molecules

A: CYTOCHROME C
B: CYTOCHROME C
C: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,11826
Polymers73,0626
Non-polymers5,05620
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area16720 Å2
ΔGint-343.4 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.930, 110.880, 60.930
Angle α, β, γ (deg.)90.00, 131.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

21A-2028-

HOH

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Components

#1: Protein CYTOCHROME C / / CYTOCHROME C555


Mass: 12176.954 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) CRITHIDIA FASCICULATA (eukaryote) / References: UniProt: P00078
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHEME (HEM): HEME ATTACHED VIA ONLY ONE THIOETHER BOND

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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: 2.2 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.45 M (NH4)2 SO4, 0.1 M HEPES (PH 6.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9511
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9511 Å / Relative weight: 1
ReflectionResolution: 1.55→56 Å / Num. obs: 60049 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.56 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.8
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCC

1ycc


Resolution: 1.55→55.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.822 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 2411 4 %RANDOM
Rwork0.20634 ---
obs0.20779 57638 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.71 Å2
2---0.26 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 164 563 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.192.0623705
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83923.824102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73815393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4441515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212088
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8431.51626
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34422568
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.30631087
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3574.51137
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.552→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 171 -
Rwork0.321 4073 -
obs--93.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.89230.68130.24161.9518-0.01321.0086-0.00430.0465-0.0513-0.19870.0594-0.04280.15290.1338-0.05520.09230.0254-0.04360.0659-0.020.03615.29619.9957.673
21.67741.2970.43222.18430.8081.45430.1297-0.0509-0.13390.094-0.0676-0.0850.3011-0.0285-0.06210.13760.0036-0.07860.0162-0.00020.068912.02715.44212.945
30.8989-0.8556-0.41661.6870.43850.9085-0.02590.0274-0.15090.0682-0.12420.19690.0643-0.1450.15010.0356-0.02-0.02040.0949-0.0270.07520.40437.60622.423
42.1337-0.9074-0.20611.23360.20650.7416-0.0385-0.01790.07240.0237-0.050.0539-0.0294-0.07670.08850.03710.0158-0.04280.0909-0.04040.06460.70745.17224.138
51.5968-0.08270.03640.5974-0.24242.1642-0.09540.26620.32610.03610.01160.0536-0.18740.07670.08390.0548-0.0199-0.05480.09410.06480.108418.77946.9624.165
62.0457-0.29331.32770.7881-0.63133.12-0.09690.52170.2042-0.0115-0.0775-0.0516-0.04520.41540.17440.0321-0.0393-0.03940.20940.08080.058224.69743.9850.276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 71
2X-RAY DIFFRACTION2A72 - 114
3X-RAY DIFFRACTION3B5 - 71
4X-RAY DIFFRACTION4B72 - 114
5X-RAY DIFFRACTION5C5 - 71
6X-RAY DIFFRACTION6C72 - 114

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