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- PDB-1j0p: Three dimensional Structure of the Y43L mutant of Tetraheme Cytoc... -

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Basic information

Entry
Database: PDB / ID: 1j0p
TitleThree dimensional Structure of the Y43L mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F
ComponentsCytochrome c3
KeywordsELECTRON TRANSPORT / tetraheme cytochrome c3 / high resolution X-ray structure / Y43L mutant
Function / homology
Function and homology information


anaerobic respiration / electron transfer activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ETHANOL / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c3
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.91 Å
AuthorsOzawa, K. / Yasukawa, F. / Kumagai, J. / Ohmura, T. / Cusanvich, M.A. / Tomimoto, Y. / Ogata, H. / Higuchi, Y. / Akutsu, H.
CitationJournal: Biophys.J. / Year: 2003
Title: Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F.
Authors: Ozawa, K. / Takayama, Y. / Yasukawa, F. / Ohmura, T. / Cusanovich, M.A. / Tomimoto, Y. / Ogata, H. / Higuchi, Y. / Akutsu, H.
History
DepositionNov 19, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,02124
Polymers11,5791
Non-polymers3,44123
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.868, 67.309, 34.328
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 c3


Mass: 11579.344 Da / Num. of mol.: 1 / Mutation: Y43L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Plasmid: pKFC3K / Production host: Shewanella oneidensis (bacteria) / Strain (production host): TSP-C / References: UniProt: P00132
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.4 / Details: ethanol, pH 7.4, SMALL TUBES, temperature 277K
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
212.5 mMTris-HCl1droppH7.4
350 %(v/v)ethanol1drop
410 mMTris-HCl1reservoirpH7.4
560 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.913→26.343 Å / Num. all: 82305 / Num. obs: 82055 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.044
Reflection shellResolution: 0.91→0.96 Å / Rmerge(I) obs: 0.221 / % possible all: 88.1
Reflection
*PLUS
Highest resolution: 0.91 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
SHELXL-97refinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2CDV

2cdv


Resolution: 0.91→10 Å / Num. parameters: 13084 / Num. restraintsaints: 14462 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.136 5786 -RANDOM
Rwork0.0994 ---
all0.1078 81910 --
obs0.1015 67354 88.7 %-
Refine analyzeLuzzati coordinate error obs: 0.035 Å / Num. disordered residues: 2 / Occupancy sum hydrogen: 1019 / Occupancy sum non hydrogen: 1393.98
Refinement stepCycle: LAST / Resolution: 0.91→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 188 422 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.028
X-RAY DIFFRACTIONs_angle_d0.053
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0316
X-RAY DIFFRACTIONs_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.084
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.094
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.136 / Rfactor Rwork: 0.1057
Solvent computation
*PLUS
Displacement parameters
*PLUS

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