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- PDB-7tbq: LOV2-DARPIN fusion : D7 -

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Basic information

Entry
Database: PDB / ID: 7tbq
TitleLOV2-DARPIN fusion : D7
ComponentsD7 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: 2.678 Å
AuthorsMittl, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LOV2-DARPIN fusion : D7
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

Downloads & links

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Assembly

Deposited unit
A: D7 LOV2-DARPin fusion
B: D7 LOV2-DARPin fusion
C: D7 LOV2-DARPin fusion
D: D7 LOV2-DARPin fusion
E: D7 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,20720
Polymers206,3895
Non-polymers2,81815
Water36020
1
A: D7 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8504
Polymers41,2781
Non-polymers5733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D7 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8865
Polymers41,2781
Non-polymers6084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D7 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8504
Polymers41,2781
Non-polymers5733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D7 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8865
Polymers41,2781
Non-polymers6084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: D7 LOV2-DARPin fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7342
Polymers41,2781
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.212, 93.212, 233.136
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
D7 LOV2-DARPin fusion


Mass: 41277.734 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 35 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium chloride, 25% PEG3350, 100 mM 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: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→80.72 Å / Num. obs: 56150 / % possible obs: 94 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.034 / Rrim(I) all: 0.11 / Net I/σ(I): 12.8
Reflection shellResolution: 2.68→2.82 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2813 / CC1/2: 0.571 / % possible all: 48.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TBN

7tbn


Resolution: 2.678→38.14 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.436
RfactorNum. reflection% reflectionSelection details
Rfree0.2949 2665 -RANDOM
Rwork0.2391 ---
obs0.2418 56129 88.1 %-
Displacement parametersBiso mean: 105 Å2
Baniso -1Baniso -2Baniso -3
1--1.6711 Å20 Å20 Å2
2---1.6711 Å20 Å2
3---3.3421 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.678→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14460 0 185 20 14665
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00817812HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9724144HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6330SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3230HARMONIC5
X-RAY DIFFRACTIONt_it17812HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2360SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact13938SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion21.03
LS refinement shellResolution: 2.68→2.76 Å
RfactorNum. reflection% reflection
Rfree0.3727 42 -
Rwork0.2857 --
obs0.2887 1123 20.16 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08960.67520.37352.4927-0.50572.08160.47440.4113-0.03490.4113-0.2743-0.2263-0.0349-0.2263-0.20020.1203-0.2359-0.1277-0.04160.0622-0.027139.380244.5909-21.1284
20.3485-0.13940.61912.0958-1.22162.8912-0.0997-0.81650.6622-0.81650.4812-0.21950.6622-0.2195-0.38160.1275-0.2682-0.2398-0.02990.0950.067420.0712.0065-19.0418
32.4074-0.3933-0.36710.67020.46642.14-0.04850.053-0.2170.0530.21110.0471-0.2170.0471-0.1626-0.2041-0.0595-0.00610.2749-0.1457-0.0044-11.698815.437820.8113
41.7612-0.7308-0.92430.75431.27723.26190.0367-0.03380.1494-0.03380.40840.71660.14940.7166-0.4451-0.222-0.0361-0.0350.3266-0.27270.076734.886510.815718.8815
50.1853-0.1124-0.67960.1611-0.40452.01770.1423-0.0492-0.9144-0.04920.1237-0.5461-0.9144-0.5461-0.2660.33580.17370.05060.23760.05270.21977.761540.80060.108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A400 - 774
2X-RAY DIFFRACTION1{ A|* }A803 - 804
3X-RAY DIFFRACTION2{ B|* }B400 - 774
4X-RAY DIFFRACTION2{ B|* }B803 - 804
5X-RAY DIFFRACTION3{ C|* }C400 - 774
6X-RAY DIFFRACTION3{ C|* }C803 - 804
7X-RAY DIFFRACTION4{ D|* }D400 - 774
8X-RAY DIFFRACTION4{ D|* }D803 - 804
9X-RAY DIFFRACTION5{ E|* }E404 - 774
10X-RAY DIFFRACTION5{ E|* }E803

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