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- PDB-7tcd: LOV2-DARPIN fusion: D13 -

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Basic information

Entry
Database: PDB / ID: 7tcd
TitleLOV2-DARPIN fusion: D13
ComponentsD13 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: 1.7 Å
AuthorsMittl, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LOV2-DARPIN fusion: D13
Authors: Mittl, P. / Plueckthun, A.
History
DepositionDec 23, 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: D13 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5295
Polymers48,9771
Non-polymers5524
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.504, 47.902, 78.068
Angle α, β, γ (deg.)90.000, 107.560, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein D13 LOV2-DARPin fusion


Mass: 48977.402 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M sodium chloride 28% PEG4000 100 mM sodium citrate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→45.07 Å / Num. obs: 31319 / % possible obs: 83.5 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.041 / Rrim(I) all: 0.079 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.97 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1567 / CC1/2: 0.712 / % possible all: 35.9

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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: 7TAL

7tal


Resolution: 1.7→45.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.303 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 1550 4.9 %RANDOM
Rwork0.1814 ---
obs0.1849 29768 57.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.38 Å2 / Biso mean: 27.725 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.39 Å2
2--0.98 Å20 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.7→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 34 246 3675
Biso mean--20.19 35.22 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133473
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173406
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.6414697
X-RAY DIFFRACTIONr_angle_other_deg1.4411.5867823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13422.5196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80715630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.451529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02757
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 4 -
Rwork0.222 80 -
all-84 -
obs--2.12 %
Refinement TLS params.Method: refined / Origin x: 28.41 Å / Origin y: -11.184 Å / Origin z: 17.306 Å
111213212223313233
T0.0012 Å20.0015 Å2-0.0019 Å2-0.0066 Å2-0.0049 Å2--0.0075 Å2
L0.1038 °20.0225 °20.0254 °2-0.0239 °2-0.009 °2--0.0173 °2
S0.0021 Å °-0.0105 Å °-0.0033 Å °-0.0013 Å °0.0007 Å °0.0018 Å °0.0018 Å °-0.0044 Å °-0.0028 Å °

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