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- PDB-1fcd: THE STRUCTURE OF FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE FROM A P... -

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Entry
Database: PDB / ID: 1fcd
TitleTHE STRUCTURE OF FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE FROM A PURPLE PHOTOTROPHIC BACTERIUM CHROMATIUM VINOSUM AT 2.5 ANGSTROMS RESOLUTION
Components
  • FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (CYTOCHROME SUBUNIT)
  • FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FLAVIN-BINDING SUBUNIT)
KeywordsELECTRON TRANSPORT(FLAVOCYTOCHROME)
Function / homology
Function and homology information


sulfide-cytochrome-c reductase (flavocytochrome c) / sulfide dehydrogenase activity / flavin adenine dinucleotide binding / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain superfamily / : / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central / : / TAT (twin-arginine translocation) pathway signal sequence / Cytochrome c4-like ...Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Flavocytochrome c sulphide dehydrogenase, flavin-binding domain superfamily / : / Flavocytochrome c sulphide dehydrogenase, flavin-binding / Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain, central / : / TAT (twin-arginine translocation) pathway signal sequence / Cytochrome c4-like / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / FAD/NAD-linked reductase, dimerisation domain superfamily / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / HEME C / Cytochrome subunit of sulfide dehydrogenase / Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.53 Å
AuthorsChen, Z.W. / Koh, M. / Van Driessche, G. / Van Beeumen, J.J. / Bartsch, R.G. / Meyer, T.E. / Cusanovich, M.A. / Mathews, F.S.
Citation
Journal: Science / Year: 1994
Title: The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium.
Authors: Chen, Z.W. / Koh, M. / Van Driessche, G. / Van Beeumen, J.J. / Bartsch, R.G. / Meyer, T.E. / Cusanovich, M.A. / Mathews, F.S.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Nucleotide Sequence of the Heme Subunit of Flavocytochrome C from the Purple Phototrophic Bacterium, Chromatium Vinosum
Authors: Dolata, M.M. / Van Beeumen, J.J. / Ambler, R.P. / Meyer, T.E. / Cusanovich, M.A.
#2: Journal: Chemistry and Biochemistry of Flavoenzymes / Year: 1991
Title: Flavocytochrome C
Authors: Cusanovich, M.A. / Meyer, T.E. / Bartsch, R.G.
History
DepositionAug 18, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650HELIX FLAVOPROTEIN SUBUNIT CONTAINS HELICES 1 - 22 IN *HELIX* RECORDS BELOW. CYTOCHROME SUBUNIT ...HELIX FLAVOPROTEIN SUBUNIT CONTAINS HELICES 1 - 22 IN *HELIX* RECORDS BELOW. CYTOCHROME SUBUNIT CONTAINS HELICES 23 - 38 IN *HELIX* RECORDS BELOW.
Remark 700SHEET THERE ARE TWO BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH ...SHEET THERE ARE TWO BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *A8* AND *A9* REPRESENT ONE BIFURCATED SHEET. SHEETS *B8* AND *B9* REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FLAVIN-BINDING SUBUNIT)
C: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (CYTOCHROME SUBUNIT)
B: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FLAVIN-BINDING SUBUNIT)
D: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (CYTOCHROME SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,19710
Polymers124,1524
Non-polymers4,0456
Water00
1
A: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FLAVIN-BINDING SUBUNIT)
C: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (CYTOCHROME SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0985
Polymers62,0762
Non-polymers2,0233
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-75 kcal/mol
Surface area21460 Å2
MethodPISA
2
B: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FLAVIN-BINDING SUBUNIT)
D: FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (CYTOCHROME SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0985
Polymers62,0762
Non-polymers2,0233
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-74 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.600, 84.600, 106.400
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 223
2: PHE A 400 - GLY A 401 OMEGA = 123.04 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO C 24 / 4: CIS PROLINE - PRO B 223 / 5: CIS PROLINE - PRO D 24
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7707, 0.0185, -0.6369), (-0.0229, -0.9997, -0.0014), (-0.6368, 0.0135, 0.7709)
Vector: 79.55, -19.28, 28.77)
DetailsA NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS EXISTS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *C* WHEN APPLIED TO CHAINS *B* AND *D*, RESPECTIVELY.

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Components

#1: Protein FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (FLAVIN-BINDING SUBUNIT)


Mass: 42844.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / References: UniProt: Q06530
#2: Protein FLAVOCYTOCHROME C SULFIDE DEHYDROGENASE (CYTOCHROME SUBUNIT)


Mass: 19231.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / References: UniProt: Q06529
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Compound detailsTHE ACTIVE SITE OF THE FLAVOPROTEIN SUBUNIT CONTAINS A CATALYTICALLY IMPORTANT DISULFIDE BRIDGE ...THE ACTIVE SITE OF THE FLAVOPROTEIN SUBUNIT CONTAINS A CATALYTICALLY IMPORTANT DISULFIDE BRIDGE LOCATED ABOVE THE PYRIMIDINE PORTION OF THE FLAVIN RING. ANY OF A TRYPTOPHAN, THREONINE OR TYROSINE SIDE CHAIN MAY PROVIDE A PARTIAL CONDUIT FOR ELECTRON TRANSFER TO ONE OF THE HEME GROUPS LOCATED 9.9 A FROM THE FLAVIN.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal grow
*PLUS
pH: 7.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
145 mg/mlprotein11
20.02 MTris-HCl11
30.5 M11NaCl
465 %satammonium sulfate12

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.53 Å / % possible obs: 95 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.237 / Rfactor obs: 0.237 / Highest resolution: 2.53 Å
Details: RESIDUES 1 - 174 OF THE CYTOCHROME SUBUNIT AND RESIDUES 1 - 95 OF THE FLAVOPROTEIN SUBUNIT WERE OBTAINED FROM THE DNA SEQUENCE. RESIDUES 96 TO THE END OF THE FLAVOPROTEIN SUBUNIT WERE ...Details: RESIDUES 1 - 174 OF THE CYTOCHROME SUBUNIT AND RESIDUES 1 - 95 OF THE FLAVOPROTEIN SUBUNIT WERE OBTAINED FROM THE DNA SEQUENCE. RESIDUES 96 TO THE END OF THE FLAVOPROTEIN SUBUNIT WERE OBTAINED FROM PRELIMINARY PEPTIDE FRAGMENT SEQUENCES WHICH WERE ALIGNED BY CORRELATION WITH THE EXPERIMENTAL X-RAY MAP.
Refinement stepCycle: LAST / Highest resolution: 2.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8724 0 278 0 9002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.8
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.8

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