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- PDB-1ofy: three dimensional structure of the reduced form of nine-heme cyto... -

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Basic information

Entry
Database: PDB / ID: 1ofy
Titlethree dimensional structure of the reduced form of nine-heme cytochrome c at ph 7.5
ComponentsNINE HEME CYTOCHROME C
KeywordsELECTRON TRANSPORT / MULTIHEME CYTOCHROME C / ELECTRON TRANSFER
Function / homology
Function and homology information


periplasmic space / electron transfer activity / 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
ACETATE ION / HEME C / Nine-heme cytochrome c
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBento, I. / Teixeira, V.H. / Baptista, A.M. / Soares, C.M. / Matias, P.M. / Carrondo, M.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Redox-Bohr and Other Cooperativity Effects in the Nine-Heme Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies
Authors: Bento, I. / Teixeira, V.H. / Baptista, A.M. / Soares, C.M. / Matias, P.M. / Carrondo, M.A.
History
DepositionApr 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,90423
Polymers64,5282
Non-polymers11,37621
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.400, 105.660, 80.940
Angle α, β, γ (deg.)90.00, 103.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NINE HEME CYTOCHROME C / 9HCC


Mass: 32264.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q9RN68
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop / Details: Coelho, A.V., (1996) Protein Sci., 5, 1189.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(w/v)PEG40001reservoir
20.1 MHEPES1reservoir
30.2 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 65158 / % possible obs: 97.6 % / Redundancy: 2.72 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.69 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / Redundancy: 2.72 % / Num. measured all: 177499 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 98 % / Rmerge(I) obs: 0.371

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 19HC

19hc


Resolution: 2→25 Å / Num. parameters: 23131 / Num. restraintsaints: 28791 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 3242 5.2 %RANDOM
all0.2416 61844 --
obs0.2151 -92.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 9 / Occupancy sum non hydrogen: 5701
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 790 505 5719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0.048
X-RAY DIFFRACTIONs_from_restr_planes0.275
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.049
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.237 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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