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- PDB-1ag9: FLAVODOXINS THAT ARE REQUIRED FOR ENZYME ACTIVATION: THE STRUCTUR... -

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Basic information

Entry
Database: PDB / ID: 1ag9
TitleFLAVODOXINS THAT ARE REQUIRED FOR ENZYME ACTIVATION: THE STRUCTURE OF OXIDIZED FLAVODOXIN FROM ESCHERICHIA COLI AT 1.8 ANGSTROMS RESOLUTION.
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / REDUCTIVE ACTIVATION / FLAVODOXIN / ESCHERICHIA COLI
Function / homologyFlavodoxin, conserved site / Flavodoxin/nitric oxide synthase / Flavodoxin, long chain / Flavoprotein-like superfamily / Flavodoxin / Flavodoxin signature. / Flavodoxin-like domain profile. / FMN binding / electron transfer activity / cytosol ...Flavodoxin, conserved site / Flavodoxin/nitric oxide synthase / Flavodoxin, long chain / Flavoprotein-like superfamily / Flavodoxin / Flavodoxin signature. / Flavodoxin-like domain profile. / FMN binding / electron transfer activity / cytosol / cytoplasm / Flavodoxin 1
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.8 Å resolution
AuthorsHoover, D.M. / Ludwig, M.L.
CitationJournal: Protein Sci. / Year: 1997
Title: A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Escherichia coli at 1.8 A resolution.
Authors: Hoover, D.M. / Ludwig, M.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 4, 1997 / Release: Dec 24, 1997
RevisionDateData content typeGroupProviderType
1.0Dec 24, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAVODOXIN
B: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,90216
Polyers39,2472
Non-polymers1,65414
Water6,377354
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4210
ΔGint (kcal/M)-117
Surface area (Å2)14850
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)126.400, 41.100, 68.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide FLAVODOXIN /


Mass: 19623.674 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Strain: DHALPHA / Cellular location: CYTOPLASM / Gene: FLDA / Plasmid name: PDH01 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P61949

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Non-polymers , 6 types, 368 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Formula: Ca / Calcium
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Formula: Cl / Chloride
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Formula: Na / Sodium
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Formula: C17H21N4O9P / Flavin mononucleotide
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Formula: C8H19NO5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Formula: H2O / Water

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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: 2.2 / Density percent sol: 44.1 %
Crystal growTemp: 295 K / pH: 7
Details: PROTEIN WAS CRYSTALLIZED BY MICROSEEDING IN 40% MPD, 100 MM CACL2, 20 MM BIS-TRIS, 10 MM IMIDAZOLE, PH 7.0, 295 K.
Crystal grow
*PLUS
Temp: 22 ℃ / Method: vapor diffusion, hanging drop / Details: microseeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
17.5-10 mg/mlprotein1drop
210 mMimidazole1drop
320 %MPD1drop
450 mM1dropCaCl2
510 mMBis-Tris1drop
640 %MPD1reservoir
7100 mM1reservoirCaCl2
820 mMBis-Tris1reservoir
910 mMimidazole1reservoir

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Data collection

DiffractionMean temperature: 140 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Details: COLLIMATOR / Detector: AREA DETECTOR / Collection date: Dec 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 15.7 Å2 / D resolution high: 1.8 Å / D resolution low: 35 Å / Number obs: 32752 / Observed criterion sigma I: 0 / Rsym value: 0.072 / NetI over sigmaI: 26.3 / Redundancy: 6.6 % / Percent possible obs: 97.1
Reflection shellHighest resolution: 1.8 Å / Lowest resolution: 1.88 Å / MeanI over sigI obs: 5.9 / Rsym value: 0.166 / Redundancy: 3.8 % / Percent possible all: 93.4
Reflection
*PLUS
Number measured all: 213264 / Rmerge I obs: 0.072
Reflection shell
*PLUS
Percent possible obs: 93.4 / Rmerge I obs: 0.166

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OFV
Details: RESIDUES 170 - 176 ARE PARTIALLY DISORDERED AND WERE MODELED USING INFORMATION FROM A DIFFERENT CRYSTAL FORM OF A HIS-TAGGED MUTANT.
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Cross valid method: A POSTERIORI / Sigma F: 0
Displacement parametersB iso mean: 25 Å2 / Aniso B11: 3.8865 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0.4394 Å2 / Aniso B23: 0 Å2 / Aniso B33: 3.4471 Å2
Least-squares processR factor R free: 0.25 / R factor R free error: 0.004 / R factor R work: 0.196 / R factor obs: 0.196 / Highest resolution: 1.8 Å / Lowest resolution: 1 Å / Number reflection R free: 3203 / Number reflection obs: 32072 / Percent reflection R free: 9.99 / Percent reflection obs: 95.7
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 1 Å / Luzzati sigma a free: 0.19 Å / Luzzati sigma a obs: 0.21 Å
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 2770 / Nucleic acid: 0 / Ligand: 100 / Solvent: 354 / Total: 3224
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.651.50
X-RAY DIFFRACTIONx_mcangle_it3.442.00
X-RAY DIFFRACTIONx_scbond_it2.992.00
X-RAY DIFFRACTIONx_scangle_it13.792.50
Refine LS shellHighest resolution: 1.8 Å / R factor R free: 0.296 / R factor R free error: 0.015 / R factor R work: 0.261 / Lowest resolution: 1.88 Å / Number reflection R free: 391 / Number reflection R work: 3266 / Total number of bins used: 8 / Percent reflection R free: 10.7 / Percent reflection obs: 88.93
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Least-squares process
*PLUS
R factor all: 0.202
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28
Refine LS shell
*PLUS
R factor obs: 0.261

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