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- PDB-7qnl: LOV2-DARPIN FUSION - D4_DeltaLOV -

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Basic information

Entry
Database: PDB / ID: 7qnl
TitleLOV2-DARPIN FUSION - D4_DeltaLOV
ComponentsDARPIN
KeywordsDE NOVO PROTEIN / DARPin / light switching / LOV2 domain
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsMittl, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LOV2-DARPIN FUSION - D4_DeltaLOV
Authors: Mittl, P.R.E.
History
DepositionDec 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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
AAA: DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,87511
Polymers25,9141
Non-polymers96110
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.741, 89.741, 69.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11AAA-1060-

HOH

21AAA-1064-

HOH

31AAA-1067-

HOH

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Components

#1: Protein DARPIN


Mass: 25914.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DARPin off7 with linker / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulphate, 2% PEG400, 100 mM HEPES, pH 7.5

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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 PILATUS3 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: 1.71→63.46 Å / Num. obs: 22744 / % possible obs: 95.8 % / Redundancy: 25.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.013 / Net I/σ(I): 28
Reflection shellResolution: 1.71→1.85 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1138 / CC1/2: 0.584

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX

1svx


Resolution: 1.71→63.456 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.895 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2635 1135 4.99 %
Rwork0.1973 21609 -
all0.2 --
obs-21609 72.417 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.097 Å20 Å2-0 Å2
2--0.097 Å2-0 Å2
3----0.194 Å2
Refinement stepCycle: LAST / Resolution: 1.71→63.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 50 167 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131916
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161838
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.6232605
X-RAY DIFFRACTIONr_angle_other_deg1.4671.5864236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69724.19493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36115334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.471159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022152
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02378
X-RAY DIFFRACTIONr_nbd_refined0.2270.2442
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21748
X-RAY DIFFRACTIONr_nbtor_refined0.1590.2934
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0270.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.29
X-RAY DIFFRACTIONr_nbd_other0.2280.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2410.29
X-RAY DIFFRACTIONr_mcbond_it1.9582.634974
X-RAY DIFFRACTIONr_mcbond_other1.9552.631973
X-RAY DIFFRACTIONr_mcangle_it2.7363.9331221
X-RAY DIFFRACTIONr_mcangle_other2.7363.9361222
X-RAY DIFFRACTIONr_scbond_it3.4753.313942
X-RAY DIFFRACTIONr_scbond_other2.9443.104903
X-RAY DIFFRACTIONr_scangle_it5.1614.7821384
X-RAY DIFFRACTIONr_scangle_other4.6564.4711325
X-RAY DIFFRACTIONr_lrange_it9.5734.0372173
X-RAY DIFFRACTIONr_lrange_other9.30233.4562131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.206100.293135X-RAY DIFFRACTION6.3708
1.75-1.7980.336170.309368X-RAY DIFFRACTION17.2414
1.798-1.850.383270.299594X-RAY DIFFRACTION28.9241
1.85-1.9070.279540.279777X-RAY DIFFRACTION39.4774
1.907-1.970.266530.255979X-RAY DIFFRACTION50.8124
1.97-2.0390.221750.231244X-RAY DIFFRACTION66.0822
2.039-2.1150.268870.2311614X-RAY DIFFRACTION89.3852
2.115-2.2020.283910.2321752X-RAY DIFFRACTION100
2.202-2.30.216740.2151705X-RAY DIFFRACTION99.9438
2.3-2.4120.237910.1981618X-RAY DIFFRACTION100
2.412-2.5420.308790.2071534X-RAY DIFFRACTION100
2.542-2.6960.257730.2071449X-RAY DIFFRACTION100
2.696-2.8820.29690.2051381X-RAY DIFFRACTION100
2.882-3.1120.315720.2061287X-RAY DIFFRACTION99.9265
3.112-3.4080.348650.2021181X-RAY DIFFRACTION99.9198
3.408-3.8090.214620.1741095X-RAY DIFFRACTION99.9136
3.809-4.3960.232480.158969X-RAY DIFFRACTION99.9018
4.396-5.3770.234400.165841X-RAY DIFFRACTION100
5.377-7.5770.204320.218670X-RAY DIFFRACTION99.8577
7.577-63.4560.39160.19416X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.5371 Å / Origin y: -5.6868 Å / Origin z: 13.0663 Å
111213212223313233
T0.0936 Å2-0.0011 Å20.016 Å2-0.0221 Å20.0122 Å2--0.0514 Å2
L0.4949 °2-0.1724 °20.0121 °2-0.816 °20.6032 °2--0.4987 °2
S-0.1842 Å °0.0084 Å °-0.0326 Å °0.0038 Å °0.1034 Å °0.0719 Å °-0.0516 Å °0.0797 Å °0.0808 Å °
Refinement TLS groupSelection: ALL

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