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- PDB-3car: REDUCED STRUCTURE OF THE ACIDIC CYTOCHROME C3 FROM DESULFOVIBRIO ... -

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Basic information

Entry
Database: PDB / ID: 3car
TitleREDUCED STRUCTURE OF THE ACIDIC CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / CYTOCHROME C3 / TETRAHEME / REDUCED FORM / DESULFOVIBRIO AFRICANUS
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 c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ARSENIC / PROTOPORPHYRIN IX CONTAINING FE / Acidic cytochrome c3
Similarity search - Component
Biological speciesDesulfovibrio africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNorager, S. / Legrand, P. / Pieulle, L. / Hatchikian, C. / Roth, M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the oxidised and reduced acidic cytochrome c3from Desulfovibrio africanus.
Authors: Norager, S. / Legrand, P. / Pieulle, L. / Hatchikian, C. / Roth, M.
#1: Journal: Thesis, Universite Joseph Fourier / Year: 1998
Title: Crystallographic Studies of the Two Tetraheme Cytochromes C3 from Desulfovibrio Africanus
Authors: Norager, S.C.
#2: Journal: Biochim.Biophys.Acta / Year: 1997
Title: Further Characterization of the Two Tetraheme Cytochromes C3 from Desulfovibrio Africanus: Nucleotide Sequences, Epr Spectroscopy and Biological Activity
Authors: Magro, V. / Pieulle, L. / Forget, N. / Guigliarelli, B. / Petillot, Y. / Hatchikian, E.C.
#3: Journal: Biochim.Biophys.Acta / Year: 1996
Title: Biochemical Studies of the C-Type Cytochromes of the Sulfate Reducer Desulfovibrio Africanus. Characterization of Two Tetraheme Cytochromes C3 with Different Specificity
Authors: Pieulle, L. / Haladjian, J. / Bonicel, J. / Hatchikian, E.C.
History
DepositionNov 17, 1998Processing site: BNL
Revision 1.0Jul 23, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Apr 3, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,23112
Polymers11,2781
Non-polymers2,95211
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CYTOCHROME C3
hetero molecules

A: CYTOCHROME C3
hetero molecules

A: CYTOCHROME C3
hetero molecules

A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,92348
Polymers45,1134
Non-polymers11,80944
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area24070 Å2
ΔGint-920 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.657, 107.657, 107.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-110-

ARS

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Components

#1: Protein CYTOCHROME C3


Mass: 11278.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio africanus (bacteria) / Cellular location: PERIPLASM / Strain: BENGHAZI / References: UniProt: P94690
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 74.922 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: As
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.34 Å3/Da / Density % sol: 67 %
Crystal growpH: 5.8 / Details: pH 5.80
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
PH range low: 5.8 / PH range high: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
26-8 %(w/v)PEG80001reservoir
30.05 Mzinc acetate1reservoir
40.1 Mcacodylate 1reservoir

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Data collection

DiffractionMean temperature: 108.2 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.0057
DetectorType: THOMSON/PRINCETON JNSJR / Detector: CCD AREA DETECTOR / Date: Jan 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0057 Å / Relative weight: 1
ReflectionResolution: 1.85→29 Å / Num. obs: 17501 / % possible obs: 97.9 % / Redundancy: 32.4 % / Biso Wilson estimate: 21.12 Å2 / Rsym value: 0.065 / Net I/σ(I): 8.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.531 / % possible all: 87.4
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 87.4 % / Rmerge(I) obs: 0.531

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
XDSdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OXIDISED FORM OF THE SAME PROTEIN

Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15
Details: RESIDUES WITH AN OCCUPANCY LOWER THAN 1.0, ARE REFINED WITH THE GIVEN OCCUPANCY. THIS OCCUPANCY HAS BEEN ESTABLISHED MANUALLY TO AVOID POSITIVE OR NEGATIVE PEAKS IN THE FOBS-FCALC DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.198 ---
obs-16485 99 %-
Displacement parametersBiso mean: 29.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 179 159 1124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.033
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.035
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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