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- PDB-7tal: LOV2-DARPIN fusion : D4_deltaDARP -

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Basic information

Entry
Database: PDB / ID: 7tal
TitleLOV2-DARPIN fusion : D4_deltaDARP
ComponentsD4_deltaDARP LOV2-DARPin fusion
KeywordsDE NOVO PROTEIN / light switching
Function / homologyFLAVIN MONONUCLEOTIDE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMittl, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LOV2-DARPIN fusion : D4_deltaDARP
Authors: Mittl, P.R.
History
DepositionDec 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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Assembly

Deposited unit
A: D4_deltaDARP LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8963
Polymers22,4161
Non-polymers4812
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.142, 50.768, 87.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D4_deltaDARP LOV2-DARPin fusion


Mass: 22415.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 37.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M lithium sulphate, 2% PEG8000, pH undefined

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→43.88 Å / Num. obs: 46107 / % possible obs: 83.5 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.013 / Net I/σ(I): 20.9
Reflection shellResolution: 1.1→1.19 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2305 / CC1/2: 0.702 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V0W

2v0w


Resolution: 1.1→43.88 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.834 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2322 5 %RANDOM
Rwork0.1517 ---
obs0.1543 43785 63.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.41 Å2 / Biso mean: 18.628 Å2 / Biso min: 8.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.1→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 32 242 1851
Biso mean--11.61 33.38 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171774
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.6482444
X-RAY DIFFRACTIONr_angle_other_deg1.5571.5934092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6025227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.89821.776107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18715347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6021518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022085
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02417
X-RAY DIFFRACTIONr_rigid_bond_restr3.51433568
LS refinement shellResolution: 1.102→1.131 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 10 -
Rwork0.242 184 -
all-194 -
obs--3.66 %

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