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- PDB-1gm4: OXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURIC... -

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Basic information

Entry
Database: PDB / ID: 1gm4
TitleOXIDISED STRUCTURE OF CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 at pH 7.6
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / CYTOCHROME
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
HEME C / Class III cytochrome C family protein
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBento, I. / Louro, R. / Matias, P.M. / Catarino, T. / Baptista, A.M. / Soares, C.M. / Carrondo, M.A. / Turner, D.L. / Xavier, A.V.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome.
Authors: Louro, R.O. / Bento, I. / Matias, P.M. / Catarino, T. / Baptista, A.M. / Soares, C.M. / Carrondo, M.A. / Turner, D.L. / Xavier, A.V.
#1: Journal: Inorg.Chim.Acta / Year: 1998
Title: Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstroms Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstrom S Resolution
Authors: Simoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A.
#2: Journal: Biochemistry / Year: 1995
Title: Structure of the Tetraheme Cytochrome from Desulfovibrio Desulfuricans Atcc 27774: X-Ray Diffraction and Electron Paramagnetic Resonance Studies.
Authors: Morais, J. / Palma, P.N. / Frazao, C. / Caldeira, J. / Legall, J. / Moura, I. / Moura, J.J. / Carrondo, M.A.
History
DepositionSep 10, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 22, 2019Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_conn
Item: _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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 / 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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.5Oct 9, 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: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1896
Polymers11,6181
Non-polymers2,5705
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.490, 61.490, 105.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein CYTOCHROME C3


Mass: 11618.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q9L915
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growpH: 7.6 / Details: pH 7.60
Crystal grow
*PLUS
Method: other / Details: Morais, J., (1995) Biochemistry, 34, 12830.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→24 Å / Num. obs: 7877 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5.28 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 23 Å / Num. obs: 7949 / Num. measured all: 62904
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CYR

3cyr


Resolution: 2.05→24 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 504 6 %RANDOM
Rwork0.189 ---
obs0.189 7877 95.1 %-
Refine analyzeLuzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.05→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 177 79 1064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.91
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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