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- PDB-1akv: D95A SEMIQUINONE FLAVODOXIN MUTANT FROM D. VULGARIS -

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Basic information

Entry
Database: PDB / ID: 1akv
TitleD95A SEMIQUINONE FLAVODOXIN MUTANT FROM D. 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 ...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: 2 Å
AuthorsMccarthy, A. / Walsh, M. / Higgins, T.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin.
Authors: McCarthy, A.A. / Walsh, M.A. / Verma, C.S. / O'Connell, D.P. / Reinhold, M. / Yalloway, G.N. / D'Arcy, D. / Higgins, T.M. / Voordouw, G. / Mayhew, S.G.
#1: Journal: Thesis, National University of Ireland / Year: 1997
Title: X-Ray Crystallographic Studies on the Flavin Binding Site of Flavodoxin from Desulfovibrio Vulgaris
Authors: Mccarthy, A.
History
DepositionMay 27, 1997Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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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)16,5016
Polymers15,6601
Non-polymers8415
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.610, 52.610, 138.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FLAVODOXIN


Mass: 15660.137 Da / Num. of mol.: 1 / Mutation: D95A
Source method: isolated from a genetically manipulated source
Details: SEMIQUINONE
Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 / References: UniProt: P00323
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.9 Å3/Da / Density % sol: 52 %
Crystal growpH: 7 / Details: 60-70% AMMONIUM SULFATE, 100MM TRIS-HCL, PH=7.0.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-15 mg/mlprotein1drop
230-35 %satammonium sulfate1drop
350 mMTris-HCl1dropor 25mM sodium phosphate containing 1mM EDTA
460-70 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.96→10 Å / Num. obs: 13307 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.44 / Net I/σ(I): 17.5
Reflection shellResolution: 1.96→1.98 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.7 / % possible all: 97
Reflection
*PLUS
% possible obs: 99.5 % / Num. measured all: 49473
Reflection shell
*PLUS
% possible obs: 96.5 % / Rmerge(I) obs: 0.337

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Processing

Software
NameClassification
AMoREphasing
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25 805 5 %RANDOM
Rwork0.21 ---
all0.201 16098 --
obs0.2 16098 98.9 %-
Displacement parametersBiso mean: 16.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 46 137 1289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0450.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.04
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_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.283
X-RAY DIFFRACTIONp_staggered_tor18.3315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.201 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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