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- PDB-1gyo: Crystal structure of the di-tetraheme cytochrome c3 from Desulfov... -

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Basic information

Entry
Database: PDB / ID: 1gyo
TitleCrystal structure of the di-tetraheme cytochrome c3 from Desulfovibrio gigas at 1.2 Angstrom resolution
ComponentsCYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME
KeywordsELECTRON TRANSPORT / CYTOCHROME C3 / DI-TETRAHEME / AB INITIO / ELECTRON TRANSFER
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 C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome C3=26 kDa subunit of A dimeric class III C-type cytochrome
Similarity search - Component
Biological speciesDESULFOVIBRIO GIGAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.2 Å
AuthorsAragao, D. / Frazao, C. / Sieker, L. / Sheldrick, G.M. / Legall, J. / Carrondo, M.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of Dimeric Cytochrome C3 from Desulfovibrio Gigas at 1.2 A Resolution
Authors: Aragao, D. / Frazao, C. / Sieker, L. / Sheldrick, G.M. / Legall, J. / Carrondo, M.A.
#1: Journal: J.Biol.Inorg.Chem. / Year: 1999
Title: Ab Initio Structure Solution of a Dimeric Cytochrome C3 from Desulfovibrio Gigas Containing Disulfide Bridges
Authors: Frazao, C. / Sieker, L. / Sheldrick, G.M. / Lamzin, V. / Legall, J. / Carrondo, M.A.
#2: Journal: FEBS Lett. / Year: 1986
Title: Preliminary X-Ray Studies of the Tetra-Heme Cytochrome C3 and the Octa-Heme Cytochrome C3 from Desulfovibrio Gigas
Authors: Sieker, L.C. / Jensen, L.H. / Legall, J. / Carrondo, M.A.
History
DepositionApr 29, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Mar 29, 2017Group: Structure summary
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Mar 29, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME
B: CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,61412
Polymers24,4822
Non-polymers5,13210
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-192.7 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.670, 56.670, 94.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.5378, 0.8381, 0.0914), (0.8282, 0.5049, 0.2434), (0.1578, 0.2066, -0.9656)
Vector: 27.144, -17.368, 9.687)

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Components

#1: Protein CYTOCHROME C3, A DIMERIC CLASS III C-TYPE CYTOCHROME / DIMERIC CYTOCHROME C3


Mass: 12240.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO GIGAS (bacteria) / References: UniProt: Q9R638
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47.4 %
Crystal growpH: 6.5
Details: SALTING OUT FROM A PROTEIN SOLUTION IN TRIS/MALEATE PH=6.5, pH 6.50

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.1037
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1037 Å / Relative weight: 1
ReflectionResolution: 1.2→26.44 Å / Num. obs: 104411 / % possible obs: 98.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.3
Reflection shellResolution: 1.2→1.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.8 / % possible all: 95.6
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.2→26.5 Å / Num. parameters: 21173 / Num. restraintsaints: 50776 / Cross valid method: THROUGHOUT / σ(F): 0
StereochEM target val spec case: HEME GROUPS WERE RESTRAINED TO BE SIMILAR BUT WITHOUT TARGET VALUES, DUE TO THEIR INTERNAL SYMMETRY AND FOUR- OR EIGHT-FOLD REDUNDANCY
Stereochemistry target values: ENGH & HUBER
Details: C-TERMINI RESIDUES ALA107-GLN108- LYS109 ARE MISSING IN EACH MONOMER AS THEY ARE NOT VISIBLE IN ELECTRON DENSITY MAPS. SOLVENT WATER MOLECULES THAT FOLLOW THE INTER-MONOMERS NCS RELATIONSHIP ...Details: C-TERMINI RESIDUES ALA107-GLN108- LYS109 ARE MISSING IN EACH MONOMER AS THEY ARE NOT VISIBLE IN ELECTRON DENSITY MAPS. SOLVENT WATER MOLECULES THAT FOLLOW THE INTER-MONOMERS NCS RELATIONSHIP ARE DIVIDED INTO TWO CHAINS, X FOR THOSE CLOSE TO MONOMER A AND Y FOR THOSE CLOSE TO MONOMER B. OTHER SOLVENT MOLECULES ARE ASSIGNED TO CHAIN Z. THE GLYCEROL MOLECULES IN THE STRUCTURE ARE ARTIFACTS OF THE CRYO- PROTECTANT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1568 3620 3.5 %SHELLS
all0.1312 104729 --
obs0.1303 -98.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 19 / Occupancy sum non hydrogen: 2286
Refinement stepCycle: LAST / Resolution: 1.2→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 356 280 2286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes0.0292
X-RAY DIFFRACTIONs_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.103
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Rfactor obs: 0.124 / Rfactor Rfree: 0.148 / Rfactor Rwork: 0.124
Solvent computation
*PLUS
Displacement parameters
*PLUS

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