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- PDB-1obv: Y94F flavodoxin from Anabaena -

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Basic information

Entry
Database: PDB / ID: 1obv
TitleY94F flavodoxin from Anabaena
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSFER / FLAVOPROTEIN / ELECTRON 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin / Flavodoxin
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRomero, A. / Ramon, A. / Fernandez-Cabrera, C. / Irun, M.P. / Sancho, J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: How Fmn Binds to Anabaena Apoflavodoxin: A Hydrophobic Encounter at an Open Binding Site
Authors: Lostao, A. / Daoudi, F. / Irun, M.P. / Ramon, A. / Fernandez-Cabrera, C. / Romero, A. / Sancho, J.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Closure of a Tyrosine/Tryptophane Aromatic Gate Leeds to a Compact Fold in Apoflavodoxin
Authors: Genzor, C.G. / Perales-Alcon, A. / Sancho, J. / Romero, A.
History
DepositionJan 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Database references
Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / struct_ref_seq
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)19,5605
Polymers18,8161
Non-polymers7454
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.086, 57.146, 58.930
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: 18815.529 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7119 / Cell line: E.COLI JM109 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: P11241, UniProt: P0A3E0*PLUS
#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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION TYR 94 PHE THE PROTEIN IS A LOW-POTENTIAL ELECTRON DONOR TO A NUMBER OF ENZYMES. ...ENGINEERED MUTATION TYR 94 PHE THE PROTEIN IS A LOW-POTENTIAL ELECTRON DONOR TO A NUMBER OF ENZYMES. MEMBER OF THE FLAVODOXIN FAMILY
Sequence detailsTHE FIRST RESIDUE WAS MUTATED TO ALA (FROM SER) DURING CLONING PROCEDURE AS DESCRIBED IN THE ...THE FIRST RESIDUE WAS MUTATED TO ALA (FROM SER) DURING CLONING PROCEDURE AS DESCRIBED IN THE FOLLOWING ARTICLE, FILLAT ET AL., BIOCHEM. J. (1991),280,187

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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 Å3/Da / Density % sol: 37.1 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
23.2 Mammonium sulfate1reservoir
30.1 MTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.0489
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0489 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 11736 / % possible obs: 98 % / Redundancy: 3.1 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 2.1 / % possible all: 86.2
Reflection
*PLUS
Lowest resolution: 35 Å / Num. obs: 12015 / % possible obs: 98 % / Num. measured all: 111376 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 96.2 % / Num. unique obs: 1138 / Num. measured obs: 11740 / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLV

1flv


Resolution: 2.1→34.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1203022.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS ALA1001-LYS1002 WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 965 10.7 %RANDOM
Rwork0.18 ---
obs0.18 8991 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2268 Å2 / ksol: 0.384888 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å20 Å2
2---0.6 Å20 Å2
3----1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2.1→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 46 140 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 157 10.9 %
Rwork0.157 1290 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM.FMNTOPOLOGY.FMN
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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