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- PDB-1i77: CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ESSEX 6 -

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Basic information

Entry
Database: PDB / ID: 1i77
TitleCYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ESSEX 6
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / multi-heme cytochrome c
Function / homology
Function and homology information


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 superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Class III cytochrome C family protein
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEinsle, O. / Foerster, S. / Mann, K.H. / Fritz, G. / Messerschmidt, A. / Kroneck, P.M.H.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from Desulfovibrio desulfuricans Essex 6.
Authors: Einsle, O. / Foerster, S. / Mann, K. / Fritz, G. / Messerschmidt, A. / Kroneck, P.M.
History
DepositionMar 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1035
Polymers11,6371
Non-polymers2,4664
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.37, 49.39, 70.99
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME C3


Mass: 11637.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Strain: ESSEX 6 / References: UniProt: Q9L915
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG MME 2000, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG2000 MME1reservoir
20.1 Msodium acetate1reservoir
30.2 Mammonium sulfate1reservoir
45 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→18 Å / Num. all: 9821 / Num. obs: 9654 / % possible obs: 98.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.98 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.9
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.1 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 59364
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CYR

2cyr
PDB Unreleased entry


Resolution: 1.95→18 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 781 -RANDOM
Rwork0.173 ---
all-9800 --
obs-9265 95 %-
Displacement parametersBiso mean: 29.92 Å2
Baniso -1Baniso -2Baniso -3
1--3.677 Å20 Å20 Å2
2--1.348 Å20 Å2
3---2.329 Å2
Refinement stepCycle: LAST / Resolution: 1.95→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 172 117 1099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.471
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 18 Å / σ(F): 2 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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