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- PDB-5fx2: COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE... -

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Basic information

Entry
Database: PDB / ID: 5fx2
TitleCOMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE OXIDATION STATES AT CRYOGENIC TEMPERATURES
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT
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: 1.9 Å
AuthorsWatt, W. / Watenpaugh, K.D.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures.
Authors: Watt, W. / Tulinsky, A. / Swenson, R.P. / Watenpaugh, K.D.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Cloning, Nucleotide Sequence, and Expression of the Flavodoxin Gene from Disulfovibrio Vulgaris (Hildenborough)
Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P.
#2: 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.
#3: 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.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: The Binding of Riboflavin-5-Phosphate in a Flavoprotein. Flavodoxin at 2.0-Angstroms Resolution
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972
Title: Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstroms Resolution. Resolution of the Phase Ambiguity by Anomalous Scattering
Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. / Legall, J. / Dubourdieu, M.
History
DepositionOct 17, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_residues ...pdbx_database_status / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1342
Polymers15,6781
Non-polymers4561
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.360, 51.360, 139.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-150-

HOH

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Components

#1: Protein FLAVODOXIN


Mass: 15678.109 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: FLAV_DESVH SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE MET 1 MISSING PRO 2 ALA 2 WHEN THE PROTEIN SAMPLE WAS PREPARED, BY RECOMBINANT METHODS, PRO 1 WAS REPLACED BY ALA. THIS CHANGE WAS NEEDED TO OBTAIN A SAMPLE OF SUFFICIENT QUANTITY. MET 1 NEVER APPEARS IN THE ISOLATED (WILD-TYPE) OR THIS RECOMBINANT SAMPLE.

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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: 58.03 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.2 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoir
30.7-0.9 %protein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 9999 Å / Num. all: 13516 / Num. obs: 9313 / Num. measured all: 53148 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.213 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 31 244 1377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 8694 / σ(I): 2 / Rfactor obs: 0.213 / Num. reflection all: 12471
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.040.059
X-RAY DIFFRACTIONp_planar_d0.050.057

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