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- PDB-1fx1: A CRYSTALLOGRAPHIC STRUCTURAL STUDY OF THE OXIDATION STATES OF DE... -

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Basic information

Entry
Database: PDB / ID: 1fx1
TitleA CRYSTALLOGRAPHIC STRUCTURAL STUDY OF THE OXIDATION STATES OF DESULFOVIBRIO VULGARIS FLAVODOXIN
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSFER (FLAVOPROTEIN)
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, short chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily ...Flavodoxin, short chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWatenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
Citation
Journal: Flavins and Flavoproteins / Year: 1976
Title: A Crystallographic Structural Study of the Oxidation States of Desulfovibrio Vulgaris Flavodoxin
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#1: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: Flavin Mononucleotide Conformation and Environment in Flavodoxin from Desulfovibrio Vulgaris
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: The binding of riboflavin-5'-phosphate in a flavoprotein: flavodoxin at 2.0-Angstrom resolution.
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972
Title: Structure of the oxidized form of a flavodoxin at 2.5-Angstrom resolution: resolution of the phase ambiguity by anomalous scattering.
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. / Legall, J. / Dubourdieu, M.
#4: Journal: J.Biol.Chem. / Year: 1977
Title: Amino acid sequence of Desulfovibrio vulgaris flavodoxin.
Authors: Dubourdieu, M. / Fox, J.L.
History
DepositionOct 15, 1984Processing site: BNL
Revision 1.0Jan 2, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 25, 2014Group: Database references / Other
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2902
Polymers15,8331
Non-polymers4561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.600, 51.600, 139.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: SEE REMARK 5 ABOVE.

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Components

#1: Protein FLAVODOXIN


Mass: 15833.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / References: UniProt: P00323
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.08 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2 Å
Details: SOME OF THE INTERATOMIC DISTANCES ARE SIGNIFICANTLY DIFFERENT FROM THE EXPECTED VALUES. THIS IS MAINLY DUE TO THE FACT THAT THE COORDINATES WERE MANUALLY FITTED TO THE ELECTRON DENSITY AND ...Details: SOME OF THE INTERATOMIC DISTANCES ARE SIGNIFICANTLY DIFFERENT FROM THE EXPECTED VALUES. THIS IS MAINLY DUE TO THE FACT THAT THE COORDINATES WERE MANUALLY FITTED TO THE ELECTRON DENSITY AND WERE NOT IDEALIZED OR REFINED. IN PARTICULAR THE FOLLOWING INTERATOMIC DISTANCES DEVIATE SIGNIFICANTLY FROM THE EXPECTED VALUES, RESIDUE RESIDUE ATOM1 - ATOM2 DISTANCE NAME NUMBER LYS 3 CE - NZ 2.455 ALA 38 N - CA 1.972 LEU 46 CA - C 1.905 PHE 47 N - CA 1.778 GLU 48 CA - C 2.221 LEU 55 CA - C 1.232 ASP 106 N - CA 1.233 LEU 112 CB - CA 1.719
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 31 0 1135

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