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- PDB-7ob0: Structure of RsLOV d2 variant -

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Basic information

Entry
Database: PDB / ID: 7ob0
TitleStructure of RsLOV d2 variant
ComponentsLOV protein
KeywordsSIGNALING PROTEIN / Photoreceptor / light-oxygen-voltage / flavin / Per-arnt-sim
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
PAS domain / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / LOV protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoeglich, A. / Krafft, T.G.A. / Weyand, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt FoundationSofja Kovalevskaya Award Germany
CitationJournal: J.Mol.Biol. / Year: 2021
Title: A Light-Oxygen-Voltage Receptor Integrates Light and Temperature.
Authors: Dietler, J. / Schubert, R. / Krafft, T.G.A. / Meiler, S. / Kainrath, S. / Richter, F. / Schweimer, K. / Weyand, M. / Janovjak, H. / Moglich, A.
History
DepositionApr 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LOV protein
B: LOV protein
C: LOV protein
D: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,43415
Polymers78,3044
Non-polymers2,13011
Water9,782543
1
A: LOV protein
D: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1646
Polymers39,1522
Non-polymers1,0124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LOV protein
hetero molecules

C: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2709
Polymers39,1522
Non-polymers1,1187
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.057, 77.168, 155.002
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
LOV protein


Mass: 19576.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) (bacteria)
Strain: ATCC 17025 / ATH 2.4.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1E1F8

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Non-polymers , 6 types, 554 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Imidazole pH 8.0, 22 %(w/v) PEG 1000, 0,2 M Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55587 / % possible obs: 99.6 % / Redundancy: 3.93 % / Biso Wilson estimate: 22.95 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.057 / Rsym value: 0.05 / Net I/σ(I): 17.67
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 5.53 / Num. unique obs: 8900 / CC1/2: 0.961 / Rrim(I) all: 0.254 / Rsym value: 0.253

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
pointless1.12.2data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HIA

4hia


Resolution: 1.9→42.93 Å / SU ML: 0.1948 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.0844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2181 2101 3.78 %
Rwork0.176 53479 -
obs0.1776 55580 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 140 543 6060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615789
X-RAY DIFFRACTIONf_angle_d0.91847881
X-RAY DIFFRACTIONf_chiral_restr0.0497836
X-RAY DIFFRACTIONf_plane_restr0.00891063
X-RAY DIFFRACTIONf_dihedral_angle_d15.0588860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.28581370.22313471X-RAY DIFFRACTION98.07
1.94-1.990.2591380.21273511X-RAY DIFFRACTION99.73
1.99-2.050.24041380.19053513X-RAY DIFFRACTION99.78
2.05-2.110.2321380.17673516X-RAY DIFFRACTION99.67
2.11-2.170.24311390.17913542X-RAY DIFFRACTION99.65
2.17-2.250.25711390.17743540X-RAY DIFFRACTION99.57
2.25-2.340.21121380.17653526X-RAY DIFFRACTION99.78
2.34-2.450.26921390.18173538X-RAY DIFFRACTION99.92
2.45-2.580.2281400.18833571X-RAY DIFFRACTION99.87
2.58-2.740.23061400.19013556X-RAY DIFFRACTION99.84
2.74-2.950.25111400.18773572X-RAY DIFFRACTION99.62
2.95-3.250.26771410.18883596X-RAY DIFFRACTION99.65
3.25-3.720.19811410.16573592X-RAY DIFFRACTION99.36
3.72-4.680.16221430.14473621X-RAY DIFFRACTION99.45
4.68-42.930.18471500.17193814X-RAY DIFFRACTION99.42
Refinement TLS params.

Method: refined / 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)
11.90233165851-0.12244109995-0.4307283055480.838205422729-0.06373216924261.74316419773-0.0472657432425-0.07130770237610.1105011723820.02530813444450.07111865101870.0786374629503-0.224843017675-0.3203021479530.04002606203370.1538560113140.0506886224145-0.02060994274130.153743179848-0.02916285245530.15528551232-18.98155504929.07702297247-18.7859855205
20.999385273221-0.51685789997-0.3616471485341.48372122569-0.02898164045691.259604571020.1427643025710.107239829162-0.318069527082-0.0782549290117-0.043583902686-0.2100427387910.1214726010260.4617491293010.1435912135010.07832652049220.0657232256886-0.01400418163740.197743040366-0.04938771043390.160553156291-39.8355091813-4.89152693913-2.36354143796
31.972326359190.745809953672-0.980569033681.32678509669-1.095189737662.233173228840.253102349862-0.1884581459820.1424468117570.4085587258030.1335271334380.388216095358-0.648515933025-0.5013852783040.9582981746420.2171228509860.06407086293940.05682917043410.276562342758-0.00577049964550.126020580947-14.00678736796.108448348118.7945656083
41.11876599711-0.6492558466070.3483841327192.669336126860.7729152899891.190256780490.193855670940.49131315172-0.152645743859-0.460901315126-0.126836515311-0.3068029274270.4438042730670.673059235361-0.01120660401350.3182321288720.1017528105570.02250145034120.0635766744887-0.05822279916130.121640019688.15433520226-13.1718995315-38.6219400426
50.854428272208-0.226087446222-0.03364179772260.873612484718-0.001891595982960.279415812751-0.08640801448430.1216884791660.17385772816-0.213886644527-0.0497372360065-0.0889051077137-0.0400548516510.104985485396-0.08691559511810.141569084751-0.0250987930779-0.007208029020610.0682100085664-0.02964821302010.150329813588-6.220339334915.79654269367-29.551310308
61.15541511949-0.519145349365-0.4160211632040.6413768694030.3355001245940.7711856970710.0352327404717-0.2974723416650.1109704313790.120646421023-0.0491010861423-0.154804304597-0.1329418352090.1448276819450.005411676962510.112013236007-0.0139129351988-0.004412875201730.152732057367-0.0219637254170.136469277396-49.59932286745.254459329127.14624186175
71.08948665887-0.262896690631-0.5642249584290.448145249348-0.03099221793760.9012752724590.003841525958870.072031693509-0.00757763821877-0.11197320303-0.07789944377920.0748527130847-0.0610497056993-0.188281463168-0.01960956398140.110161933378-0.003516370313820.003535398290.157143455783-0.01649663568580.106861267438-3.995452810465.012613680015.45354975187
80.77302198627-0.302082181005-0.1632392981621.018025360790.4943020343740.815518755024-0.162257466311-0.3317040250090.01756144521610.04242229484160.0396423989023-0.02867430331870.1961787369140.268175668659-0.07281667377750.1516245320230.006040093265950.00147945194010.0568057139272-0.03839435296320.1299287373812.68688867388-2.76285244439-26.4502986037
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 20 through 120)AA20 - 12020 - 120
22(chain 'B' and resid 20 through 120)BB20 - 12020 - 120
33(chain 'C' and resid 20 through 120)CC20 - 12020 - 120
44(chain 'D' and resid 20 through 120)DD20 - 12020 - 120
55(chain 'A' and resid 128 through 174)AA128 - 174128 - 174
66(chain 'B' and resid 128 through 174)BB128 - 174128 - 174
77(chain 'C' and resid 128 through 174)CC128 - 174128 - 174
88(chain 'D' and resid 128 through 174)DD128 - 174128 - 174

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