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- PDB-6c4w: Structure of the yeast Pichia membranifaciens cytochrome c -

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Basic information

Entry
Database: PDB / ID: 6c4w
TitleStructure of the yeast Pichia membranifaciens cytochrome c
Componentscytochrome c
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT (CYTOCHROME) HEMEC / yeast / Saccharomyces / Molecular replacement / Valida
Function / homology
Function and homology information


: / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesPichia membranifaciens (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMcPherson, A.
CitationJournal: to be published
Title: Characterization of two crystal forms of cytochrome c from Valida membranifaciens
Authors: Day, J. / McPherson, A.
History
DepositionJan 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
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.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8002
Polymers12,1811
Non-polymers6191
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-25 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.968, 63.715, 64.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cytochrome c


Mass: 12181.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pichia membranifaciens (yeast) / References: UniProt: A0A3B6UES8*PLUS
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: thin rectangular laths
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.25 / Details: 25% PEG 4000, 0.1 M Tris-HCl, pH 8.25 / PH range: 8.0 8.5

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Dec 25, 1990
RadiationMonochromator: Supper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 4586 / % possible obs: 95.8 % / Redundancy: 2.2 % / CC1/2: 0.951 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.133 / Rrim(I) all: 0.223 / Rsym value: 0.161 / Net I/av σ(I): 3.2 / Net I/σ(I): 3.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 436 / CC1/2: 0.747 / Rpim(I) all: 0.273 / Rrim(I) all: 0.446 / Rsym value: 0.347 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ycc

1ycc


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.812 / SU B: 32.905 / SU ML: 0.374 / Cross valid method: FREE R-VALUE / ESU R: 0.779 / ESU R Free: 0.389 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33046 235 5.1 %RANDOM
Rwork0.21641 ---
obs0.22197 4344 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.586 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.27 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 43 69 964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019931
X-RAY DIFFRACTIONr_bond_other_d0.0010.02864
X-RAY DIFFRACTIONr_angle_refined_deg1.6742.041258
X-RAY DIFFRACTIONr_angle_other_deg0.6283.0022014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7045109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71524.72236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98515164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.468153
X-RAY DIFFRACTIONr_chiral_restr0.2160.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211016
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02184
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_it1.3492.057436
X-RAY DIFFRACTIONr_mcbond_other1.342.053435
X-RAY DIFFRACTIONr_mcangle_it2.2593.07542
X-RAY DIFFRACTIONr_mcangle_other2.2573.075543
X-RAY DIFFRACTIONr_scbond_it1.7452.208495
X-RAY DIFFRACTIONr_scbond_other1.7452.209493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8553.207715
X-RAY DIFFRACTIONr_long_range_B_refined5.02523.9171107
X-RAY DIFFRACTIONr_long_range_B_other4.96823.8121105
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 28 -
Rwork0.344 267 -
obs--89.12 %
Refinement TLS params.Method: refined / Origin x: -3.6282 Å / Origin y: -2.0794 Å / Origin z: 11.8077 Å
111213212223313233
T0.1612 Å2-0.0262 Å2-0.0102 Å2-0.1857 Å2-0.0094 Å2--0.0059 Å2
L1.1799 °2-0.0023 °20.2432 °2-2.5973 °20.2107 °2--5.2029 °2
S0.0418 Å °-0.0311 Å °-0.0469 Å °0.0281 Å °-0.0617 Å °-0.079 Å °0.0555 Å °-0.1115 Å °0.0199 Å °

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