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- PDB-1azl: G61V FLAVODOXIN MUTANT FROM DESULFOVIBRIO VULGARIS -

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Basic information

Entry
Database: PDB / ID: 1azl
TitleG61V FLAVODOXIN MUTANT FROM DESULFOVIBRIO VULGARIS
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / ELECTRON TRANSFER / FLAVOPROTEIN / FMN / FLAVODOXIN / MUTANT
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 / Rossmann fold ...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 subsp. vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWalsh, M.A. / Mccarthy, A. / O'Farrell, P.A. / Voordouw, G. / Higgins, T. / Mayhew, S.G.
Citation
Journal: Biochemistry / Year: 1998
Title: Modulation of the redox potentials of FMN in Desulfovibrio vulgaris flavodoxin: thermodynamic properties and crystal structures of glycine-61 mutants.
Authors: O'Farrell, P.A. / Walsh, M.A. / McCarthy, A.A. / Higgins, T.M. / Voordouw, G. / Mayhew, S.G.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Cloning,Nucleotide Sequence,and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough)
Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P.
#3: Journal: Fems Microbiol.Lett. / Year: 1988
Title: Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough
Authors: Curley, G.P. / Voordouw, G.
#4: 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.
History
DepositionNov 18, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)16,2032
Polymers15,7461
Non-polymers4561
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.490, 88.140, 35.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein FLAVODOXIN /


Mass: 15746.225 Da / Num. of mol.: 1 / Mutation: G61V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Organ: SEED / Plasmid: PDK6 / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 / References: UniProt: P00323
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 53 %
Description: MODEL USED WAS UNSUBMITTED REFINED FLAVODOXIN FROM DESULFOVIBRIO FLAVODOXIN, IDENTICAL TO PDB ENTRY 2FX2
Crystal growMethod: macroseeding / pH: 7
Details: PROTEIN SEED CRYSTALS WERE OBTAINED FROM 60-70% AMMONIUM SULFATE, 10MM TRIS PH 7.0, 1-2% ACETONE. MACROSEEDS WERE TRANSFERRED TO THE ABOVE SOLUTION WITH NO ACETONE PRESENT., macroseeding
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11-2 %(v/v)acetone1drop
210 mMTris-HCl1drop
31 mMEDTA1drop
460-70 %ammonium sulfate1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1992 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 12653 / % possible obs: 89.2 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.49 / % possible all: 79.9
Reflection
*PLUS
Num. obs: 19560 / % possible obs: 98 % / Num. measured all: 87934 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 82.6 % / Rmerge(I) obs: 0.441

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Processing

Software
NameClassification
MERLOTphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RECOMBINANT FLAVODOXIN

Resolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.175 --
all-61954 -
obs-61954 89.3 %
Displacement parametersBiso mean: 24.5 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 31 126 1263
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.14
X-RAY DIFFRACTIONp_mcangle_it4.25
X-RAY DIFFRACTIONp_scbond_it6.76
X-RAY DIFFRACTIONp_scangle_it9.88
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.180.3
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.045
X-RAY DIFFRACTIONp_planar_d0.044

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