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- PDB-5ljp: E20K/I59A/E72K/I92A/D126K/A142V FLAVODOXIN FROM ANABAENA -

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Basic information

Entry
Database: PDB / ID: 5ljp
TitleE20K/I59A/E72K/I92A/D126K/A142V FLAVODOXIN FROM ANABAENA
ComponentsFlavodoxin
KeywordsELECTRON TRANSPORT / FLAVOPROTEIN / ELECTRON TRANSFER
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 speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMartinez-Julvez, M. / Sancho, J. / Lamazares, E.
Funding support Spain, 1items
OrganizationGrant numberCountry
ALBA synchrotron2012010062 Spain
CitationJournal: Phys Chem Chem Phys / Year: 2017
Title: Direct examination of the relevance for folding, binding and electron transfer of a conserved protein folding intermediate.
Authors: Lamazares, E. / Vega, S. / Ferreira, P. / Medina, M. / Galano-Frutos, J.J. / Martinez-Julvez, M. / Velazquez-Campoy, A. / Sancho, J.
History
DepositionJul 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,2622
Polymers18,8061
Non-polymers4561
Water2,216123
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.919, 62.911, 64.650
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: 18805.646 Da / Num. of mol.: 1 / Mutation: E20K/I59A/E72K/I92A/D126K/A142V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain ATCC 29151 / PCC 7119) (bacteria)
Gene: isiB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A3E0
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 26 % and TRIS/HCl 0,1 M, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2016 / Details: KB mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→64.65 Å / Num. obs: 62821 / % possible obs: 99 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 18.1
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.6 / CC1/2: 0.933 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1flv

1flv


Resolution: 1.1→45.09 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.421 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17605 3088 4.9 %RANDOM
Rwork0.16011 ---
obs0.1609 59664 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.933 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.74 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.1→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 31 123 1477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021385
X-RAY DIFFRACTIONr_bond_other_d0.0020.021252
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.971879
X-RAY DIFFRACTIONr_angle_other_deg0.99332886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14225.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73915229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.966154
X-RAY DIFFRACTIONr_chiral_restr0.1090.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2421.186673
X-RAY DIFFRACTIONr_mcbond_other1.2261.184672
X-RAY DIFFRACTIONr_mcangle_it1.8861.787840
X-RAY DIFFRACTIONr_mcangle_other1.8871.788841
X-RAY DIFFRACTIONr_scbond_it2.1731.403712
X-RAY DIFFRACTIONr_scbond_other2.1741.404711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2432.0211039
X-RAY DIFFRACTIONr_long_range_B_refined4.68110.7531770
X-RAY DIFFRACTIONr_long_range_B_other4.60310.5131739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 244 -
Rwork0.207 4230 -
obs--97.09 %

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