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- PDB-1i55: CYTOCHROME C (TUNA) WITH 2ZN:1FE MIXED-METAL PORPHYRINS -

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Basic information

Entry
Database: PDB / ID: 1i55
TitleCYTOCHROME C (TUNA) WITH 2ZN:1FE MIXED-METAL PORPHYRINS
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT / cytochrome c / electron transfer / zinc-porphyrin
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 / PROTOPORPHYRIN IX CONTAINING ZN / Cytochrome c
Similarity search - Component
Biological speciesThunnus thynnus (Atlantic bluefin tuna)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCrane, B.R. / Tezcan, F.A. / Winkler, J.R. / Gray, H.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Electron tunneling in protein crystals.
Authors: Tezcan, F.A. / Crane, B.R. / Winkler, J.R. / Gray, H.B.
History
DepositionFeb 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 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_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / 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_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 9, 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
Remark 600HETEROGEN The residue 1104 of HEM and residue 1105 of ZNH are alternate conformers with occupancy ...HETEROGEN The residue 1104 of HEM and residue 1105 of ZNH are alternate conformers with occupancy of 0.39 and 0.61, respectively. In similar residue 1106 of HEM and residue 1107 of ZNH are alternate conformers with occupancy 0.39 and 0.61, respectively.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,2696
Polymers22,7802
Non-polymers2,4894
Water6,666370
1
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6353
Polymers11,3901
Non-polymers1,2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6353
Polymers11,3901
Non-polymers1,2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.359, 74.359, 35.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein CYTOCHROME C /


Mass: 11390.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thunnus thynnus (Atlantic bluefin tuna) / References: UniProt: P81459
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN


Mass: 626.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32N4O4Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: (NH4)2SO4 NACL NaPi, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
170-85 %satammonium sulfate1reservoir
20.75 M1reservoirNaCl
30.1 MNaPi1reservoirpH6.0
44-10 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2→3 Å / Num. all: 11058 / Num. obs: 19049 / % possible obs: 81.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.13 / % possible all: 78.2
Reflection
*PLUS
Lowest resolution: 30 Å

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CYT

3cyt


Resolution: 2→19.64 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 381490.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Crystals contained a mixture of Zn- and Fe- porphyrins with occupancies determined from anomalous scattering measurements. Residues 1104 and 1105 and residues 1105 and 1106 were refined as ...Details: Crystals contained a mixture of Zn- and Fe- porphyrins with occupancies determined from anomalous scattering measurements. Residues 1104 and 1105 and residues 1105 and 1106 were refined as non-interacting porphyrins, reflecting the mixture of Zn and Fe cytc in the crystal lattice. No stereochemical restraints were placed on ZN or Fe interactions.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 973 6.3 %RANDOM
Rwork0.218 ---
all0.218 15434 --
obs0.218 15434 81.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.98 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 172 370 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_mcbond_it0.131.5
X-RAY DIFFRACTIONc_mcangle_it0.242
X-RAY DIFFRACTIONc_scbond_it0.112
X-RAY DIFFRACTIONc_scangle_it0.192.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.278 104 7.4 %
Rwork0.26 1301 -
obs--78.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMEWATER.TOP
X-RAY DIFFRACTION4WATER.PARAMTOPH19X.HEME
X-RAY DIFFRACTION3TOPHZN.HEME
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 6.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.23
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / % reflection Rfree: 7.4 % / Rfactor Rwork: 0.26

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