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- PDB-7obz: Structure of RsLOV D109G -

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Basic information

Entry
Database: PDB / ID: 7obz
TitleStructure of RsLOV D109G
ComponentsLOV protein
KeywordsSIGNALING PROTEIN / light-oxygen-voltage / sensory photoreceptor / 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
FLAVIN MONONUCLEOTIDE / SPERMIDINE / LOV protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 25, 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
E: LOV protein
F: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,40633
Polymers116,4126
Non-polymers3,99427
Water3,099172
1
A: LOV protein
D: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,31415
Polymers38,8042
Non-polymers1,51013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LOV protein
C: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,05011
Polymers38,8042
Non-polymers1,2469
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: LOV protein
hetero molecules

F: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0437
Polymers38,8042
Non-polymers1,2395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Unit cell
Length a, b, c (Å)90.960, 65.800, 122.720
Angle α, β, γ (deg.)90.000, 94.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
LOV protein


Mass: 19401.967 Da / Num. of mol.: 6 / Mutation: D109G
Source method: isolated from a genetically manipulated source
Details: RsLOV D109G
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) / References: UniProt: M1E1F8

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Non-polymers , 5 types, 199 molecules

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


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H19N3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.15 Å3/Da / Density % sol: 60.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 0.1 M HEPES/NaOH pH7.4; 3.4 M NaCl; 0.02 M di-spermidine-triphosphat

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 97821 / % possible obs: 99.6 % / Redundancy: 3.72 % / Biso Wilson estimate: 56.96 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.088 / Net I/σ(I): 9.32
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 15597 / CC1/2: 0.189 / Rrim(I) all: 3.44 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HIA

4hia


Resolution: 2→45.37 Å / SU ML: 0.4681 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.7384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2634 2919 2.99 %
Rwork0.2175 94561 -
obs0.2188 97480 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.1 Å2
Refinement stepCycle: LAST / Resolution: 2→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7961 0 234 172 8367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00758526
X-RAY DIFFRACTIONf_angle_d0.985911583
X-RAY DIFFRACTIONf_chiral_restr0.05011231
X-RAY DIFFRACTIONf_plane_restr0.00961550
X-RAY DIFFRACTIONf_dihedral_angle_d14.69231270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.54251180.50334449X-RAY DIFFRACTION99.05
2.03-2.070.50311450.48274355X-RAY DIFFRACTION97.47
2.07-2.110.46031390.44584491X-RAY DIFFRACTION99.19
2.11-2.150.41291420.42684476X-RAY DIFFRACTION99.61
2.15-2.190.39031410.39514512X-RAY DIFFRACTION99.83
2.19-2.240.40171350.37694451X-RAY DIFFRACTION99.59
2.24-2.290.41491400.36964486X-RAY DIFFRACTION99.27
2.29-2.350.34161380.3124514X-RAY DIFFRACTION99.81
2.35-2.410.31911380.28894493X-RAY DIFFRACTION99.81
2.41-2.480.34621380.27484485X-RAY DIFFRACTION99.53
2.48-2.560.30991390.27774493X-RAY DIFFRACTION99.74
2.56-2.650.34171400.27424516X-RAY DIFFRACTION99.83
2.65-2.760.36451410.27154516X-RAY DIFFRACTION99.61
2.76-2.880.3331400.25614500X-RAY DIFFRACTION99.81
2.88-3.040.31381400.2494529X-RAY DIFFRACTION99.66
3.04-3.230.34971400.24934519X-RAY DIFFRACTION99.51
3.23-3.480.24451400.21244540X-RAY DIFFRACTION99.77
3.48-3.830.23881400.18394521X-RAY DIFFRACTION99.72
3.83-4.380.23221410.15994559X-RAY DIFFRACTION99.49
4.38-5.510.18821410.15334561X-RAY DIFFRACTION99.51
5.52-45.370.18491430.16744595X-RAY DIFFRACTION97.77
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)
15.56664505069-0.56668605220.3851949622422.8953730607-0.03043296791363.717224430940.1421142654950.0796746140015-0.409576678457-0.0658335612166-0.08147096796790.1692276026330.328494205746-0.193267533629-0.03988787587840.35186108037-0.02234158342020.0110800189810.2821416434580.03316654064640.430763496004-12.06123162098.69658107989-16.3220820592
23.540867262030.8203232818120.6073199223633.30860122361-0.5700244684072.324720940320.0830076271412-0.1737370523650.5377362773110.2291268588220.1298581195440.685369800482-0.158410863642-0.0855172208393-0.2105590405310.4131723687480.0234537589282-0.04626148357850.343266202717-0.05397637335360.64198900035417.353734851814.6574693888-0.696797793827
35.123402279080.178096359265-0.6170152009863.79324783964-0.4522600360142.47687789659-0.0376299691446-0.33519407838-0.3090398054090.171454157685-0.194787601035-0.6763956486150.06954055586080.5002273083720.1938042223830.4571374870980.0732327826056-0.09628245273990.579050250720.05131591794730.62001181336943.2562217372-11.499777971215.2177955198
42.721950730230.570016380785-1.489297521663.80253069338-0.04114631646092.614663288280.1790896801470.3365036710660.205694422577-0.26228620966-0.244522517451-1.078780179560.005522253340111.45377086441-0.02088125913780.6233376915210.07276382254640.1737677016431.214695962830.2042730531410.74507629093916.201940499821.4569277381-42.0642870724
53.34660315401-1.003138414741.650100083224.87257324057-0.8353339947074.25164763601-0.366184595797-0.69783909031.03551723001-0.1530367487690.170551862234-0.593417811419-0.0139740911301-0.6531601896950.132691690420.611973425086-0.04418200662170.06526029522070.878486647434-0.373551977190.97922948674521.7680212917-4.25883875534-65.7834909271
62.10589218765-0.6805941808290.6376628240533.136788132680.1863325952973.41127475588-0.374609405759-0.5716322158880.05203894031810.1880440331030.209193744451-0.6342702927520.3959582069730.1064130651190.1120947756970.7030495745980.06490661778090.1823008758780.934560973582-0.1506892258941.1075895306844.969996194133.9813696651-48.0790205428
75.604369410431.748842179990.5654615017226.222309704172.104550293225.665454588480.09366725431190.148833800584-0.229871801149-0.0936122178891-0.212555807574-0.5523282362450.33267777360.6754526995270.07340965063260.5141169154070.1210902584460.07535567325580.5813973801570.06166805899370.5534192405332.907218353479.13307931603-25.0502983653
85.81505561471.458894423731.243324481175.5913699796-0.7288968005625.811189669060.0383403059448-0.0707037446610.3590452620910.2690755054180.0336851118052-0.674796399673-0.3498827800690.941842569341-0.3133160499090.4648463443770.00623415201255-0.123791485370.388444598351-0.09719321217220.57335750833931.17837173179.471225695687.756687394
98.282514987220.3141234346640.3385764554675.26437137077-0.09126755598855.90947326629-0.0489759028037-0.296876101539-0.01848036900890.5003621667670.04389055702870.706764137862-0.25565905709-0.3132120116330.03028684889020.4861045772480.0794371299806-0.02688988446840.381872699004-0.05000132598030.38996743107429.7403662207-0.86387675058414.4218764346
107.598488943391.3420826301-0.2599609716656.66350203043-1.237779739276.486065821430.2938440296410.5949978299150.687213915717-0.503642869462-0.1415526820030.350525399780.2381984561480.0834993685011-0.1236784360930.5622552981640.06543408213320.04331842906840.6589936782370.00191560252480.5295416421242.015442535312.9577296346-36.6646479579
111.52373909802-0.153500847338-0.5026032904067.44577455754-3.880036730232.25176592125-0.729518516184-1.021139012530.6036160647850.0068944710952-0.0189444555599-1.50221052931-0.2998928615330.03259368431940.184955414610.6147991059350.06443422336070.02691323686161.0750376088-0.5049788759011.2288183081934.280756482-10.6555785881-56.2533542607
120.493595326928-0.8335326960980.2382038542213.45273338173-0.309594883224.80828908573-0.220105594411-0.697362241479-0.1402196332430.1064390458140.09355632687850.289787846932-0.287101473353-0.4796011583220.111159384030.6845558314770.09381621412820.1268002956711.11257215509-0.2807603311.0628388159932.028740579544.9651678122-49.9660696128
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 'E' and resid 20 through 120)EE20 - 12020 - 120
66(chain 'F' and resid 20 through 120)FF20 - 12020 - 120
77(chain 'A' and resid 128 through 174)AA128 - 174128 - 174
88(chain 'B' and resid 128 through 174)BB128 - 174128 - 174
99(chain 'C' and resid 128 through 174)CC128 - 174128 - 174
1010(chain 'D' and resid 128 through 174)DD128 - 174128 - 174
1111(chain 'E' and resid 128 through 173)EE128 - 173128 - 173
1212(chain 'F' and resid 128 through 174)FF128 - 174128 - 174

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