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- PDB-7tbo: LOV2-DARPIN fusion : D12 -

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Basic information

Entry
Database: PDB / ID: 7tbo
TitleLOV2-DARPIN fusion : D12
ComponentsD12 LOV2-DARPin fusion
KeywordsDE NOVO PROTEIN / light switching
Function / homologyPAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsMittl, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LOV2-DARPIN fusion : D12
Authors: Mittl, P.R.
History
DepositionDec 22, 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: D12 LOV2-DARPin fusion
B: D12 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6334
Polymers76,4492
Non-polymers1842
Water5,080282
1
A: D12 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3162
Polymers38,2241
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D12 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3162
Polymers38,2241
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.356, 71.645, 78.844
Angle α, β, γ (deg.)68.570, 83.130, 90.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 338
2010B3 - 338

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Components

#1: Protein D12 LOV2-DARPin fusion


Mass: 38224.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, 17% PEG10000, 20 mM BIS-Tris, pH 5.5

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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 PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→72.78 Å / Num. obs: 22563 / % possible obs: 84 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Net I/σ(I): 6.6
Reflection shellResolution: 2.32→2.61 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1129 / CC1/2: 0.691

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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: 7TBN

7tbn


Resolution: 2.32→50.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.889 / SU B: 13.013 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 1136 5 %RANDOM
Rwork0.1962 ---
obs0.2008 21423 61.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.23 Å2 / Biso mean: 59.333 Å2 / Biso min: 19.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20.27 Å2-0.01 Å2
2--0.48 Å2-0.75 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 2.32→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 12 282 5616
Biso mean--66.21 45.38 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135434
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175300
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.6387339
X-RAY DIFFRACTIONr_angle_other_deg1.2231.58812224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5515679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15424.089291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.762151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1781528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021149
Refine LS restraints NCS

Ens-ID: 1 / Number: 10821 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.321→2.381 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.13 2 -
Rwork0.245 59 -
all-61 -
obs--2.27 %

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