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- PDB-3esy: E16KE61K Flavodoxin from Anabaena -

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Basic information

Entry
Database: PDB / ID: 3esy
TitleE16KE61K Flavodoxin from Anabaena
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / ALPHA and BETA PROTEIN / Flavoprotein / FMN / Transport
Function / homology
Function and homology information


cellular response to iron ion starvation / electron transport chain / FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold ...Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / 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 speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsHerguedas, B. / Martinez-Julvez, M. / Hermoso, J.A. / Goni, G. / Medina, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Flavodoxin: A compromise between efficiency and versatility in the electron transfer from Photosystem I to Ferredoxin-NADP(+) reductase
Authors: Goni, G. / Herguedas, B. / Hervas, M. / Peregrina, J.R. / De la Rosa, M.A. / Gomez-Moreno, C. / Navarro, J.A. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavodoxin
B: Flavodoxin
C: Flavodoxin
D: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,40010
Polymers75,3914
Non-polymers2,0106
Water5,350297
1
A: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3963
Polymers18,8481
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3042
Polymers18,8481
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3042
Polymers18,8481
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Flavodoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3963
Polymers18,8481
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.287, 74.823, 109.144
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: 18847.660 Da / Num. of mol.: 4 / Mutation: E16K, E61K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: PCC 7119 / Plasmid: pTrc99a / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P0A3E0
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 32% PEG 4000, 0.2-0.3M magnesium chloride, 0.1M Tris/HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 15, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→47.2 Å / Num. all: 24311 / Num. obs: 22468 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.387 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLV

1flv


Resolution: 2.39→22.72 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.888 / SU B: 19.204 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25043 1748 7.2 %RANDOM
Rwork0.18627 ---
obs0.19096 22468 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.39→22.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 136 297 5737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.977510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38525.915284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54415912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.0861516
X-RAY DIFFRACTIONr_chiral_restr0.0980.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024228
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22779
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23714
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7031.53362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25225240
X-RAY DIFFRACTIONr_scbond_it1.78132665
X-RAY DIFFRACTIONr_scangle_it2.8484.52270
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.393→2.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 111 -
Rwork0.262 1577 -
obs--96.84 %
Refinement TLS params.Method: refined / Origin x: 37.6871 Å / Origin y: 19.4711 Å / Origin z: 68.8769 Å
111213212223313233
T0.0067 Å20.0179 Å2-0.0099 Å2--0.0147 Å20.0042 Å2--0.0014 Å2
L0.0316 °20.0033 °2-0.0755 °2-0.0318 °20.0292 °2--0.2243 °2
S0 Å °-0.0071 Å °-0.0047 Å °-0.0003 Å °-0.0046 Å °-0.0104 Å °-0.0122 Å °-0.008 Å °0.0046 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 169
2X-RAY DIFFRACTION1B2 - 169
3X-RAY DIFFRACTION1C2 - 169
4X-RAY DIFFRACTION1D2 - 169

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