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- PDB-1i1o: ROOM TEMPERATURE CRYSTAL STRUCTURE FLAVODOXIN D. VULGARIS MUTANT ... -

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Basic information

Entry
Database: PDB / ID: 1i1o
TitleROOM TEMPERATURE CRYSTAL STRUCTURE FLAVODOXIN D. VULGARIS MUTANT Y98H AT 2.0 ANG. RESOLUTION
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / High Resolution / Redox potential / electron transfer
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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsReynolds, R.A. / Watt, W. / Watenpaugh, K.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structures and comparison of the Y98H (2.0 A) and Y98W (1.5 A) mutants of flavodoxin (Desulfovibrio vulgaris).
Authors: Reynolds, R.A. / Watt, W. / Watenpaugh, K.D.
History
DepositionFeb 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 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)16,1092
Polymers15,6531
Non-polymers4561
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.960, 61.450, 57.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FLAVODOXIN /


Mass: 15653.082 Da / Num. of mol.: 1 / Fragment: MAIN CHAIN / Mutation: Y98H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / 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.: 142 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 3.2 M Ammonium Sulfate, Tris.buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8-1.0 %protein11
23.1 Mammonium sulfate12
30.1 MTris-HCl12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Feb 4, 1991 / Details: Graphite Monochomator
RadiationMonochromator: Single Crystal Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. all: 13000 / Num. obs: 9294 / % possible obs: 90 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 1.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5
Reflection shellResolution: 2→8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.06 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameClassification
MERLOTphasing
PROFFTrefinement
FRAMBOdata collection
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Flavodoxin D.vulgaris p2a

Resolution: 2→8 Å / Isotropic thermal model: isotropic / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh and Huber
Details: Standard isotropic refinement model building on E&S ps2. Details of raw data collection no longer recoverable because of change of operating systems and media Total number of reflections not ...Details: Standard isotropic refinement model building on E&S ps2. Details of raw data collection no longer recoverable because of change of operating systems and media Total number of reflections not available, approximation given.
RfactorNum. reflectionSelection details
Rwork0.172 --
all0.22 13000 -
obs0.172 9294 -
Rfree--Rfree Not available at that time
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 31 142 1296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d2.6
Software
*PLUS
Name: PROFFT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_planar_d0.022

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