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- PDB-7zqu: A fast recovering full-length LOV protein (DsLOV) from the marine... -

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Basic information

Entry
Database: PDB / ID: 7zqu
TitleA fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - C72A mutant
ComponentsPutative blue-light photoreceptor
KeywordsSIGNALING PROTEIN / LOV domain / short LOV / PAS domain / Dimerization / Signaling blue light photoreceptor
Function / homologyPAS domain / PAS-associated, C-terminal / PAC domain profile. / PAS repeat profile. / PAS domain / PAS domain superfamily / nucleotide binding / FLAVIN MONONUCLEOTIDE / Putative blue-light photoreceptor
Function and homology information
Biological speciesDinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBatra-Safferling, R. / Granzin, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFKZ 031A16 Germany
CitationJournal: To Be Published
Title: A fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - C72A mutant
Authors: Batra-Safferling, R. / Granzin, J.
History
DepositionMay 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 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

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Assembly

Deposited unit
A: Putative blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2852
Polymers16,8291
Non-polymers4561
Water72140
1
A: Putative blue-light photoreceptor
hetero molecules

A: Putative blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5704
Polymers33,6582
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3340 Å2
ΔGint-26 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.454, 28.210, 48.018
Angle α, β, γ (deg.)90.000, 119.397, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Putative blue-light photoreceptor


Mass: 16828.855 Da / Num. of mol.: 1 / Mutation: C72A
Source method: isolated from a genetically manipulated source
Details: C72A ENGINEERED MUTATION
Source: (gene. exp.) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)
Strain: DSM 16493 / NCIMB 14021 / DFL 12 / Gene: Dshi_2006
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A8LP63
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 1.6 Å3/Da
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 0.2 M MgCl2, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 6, 2014
RadiationMonochromator: microfocus beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.75→41.84 Å / Num. obs: 11015 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.053 / Rrim(I) all: 0.136 / Net I/σ(I): 7.5
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 593 / CC1/2: 0.462 / Rpim(I) all: 0.912

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.19rc6_4061refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KUK

4kuk


Resolution: 1.75→41.84 Å / SU ML: 0.2961 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205 539 4.9 %
Rwork0.1878 10467 -
obs0.1886 11006 99.65 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.81 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 31 40 996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063987
X-RAY DIFFRACTIONf_angle_d0.84731350
X-RAY DIFFRACTIONf_chiral_restr0.0536147
X-RAY DIFFRACTIONf_plane_restr0.0073180
X-RAY DIFFRACTIONf_dihedral_angle_d12.1049384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.890.36481130.30512053X-RAY DIFFRACTION98.9
1.89-2.070.31350.22932046X-RAY DIFFRACTION99.77
2.08-2.380.21581070.21412075X-RAY DIFFRACTION99.77
2.38-2.990.1931770.19782123X-RAY DIFFRACTION99.86
2.99-41.840.16581070.15632170X-RAY DIFFRACTION99.91
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)
15.549072139370.05354860913161.916614127953.46062954945-0.8953206292027.60573012032-0.1214569224260.2308615235550.607314124217-0.389432095812-0.05970890900780.491582949221-0.444605981329-0.3311527871150.1934965075840.1895340088890.0187229424826-0.006283564344040.2270814753020.002235086583540.24557718159413.65907747294.83807558042-11.521711068
27.3566850933-1.33540610860.01663484989111.552763349880.3114483654511.98350111980.04680375250180.140664906237-0.535890979988-0.0064852911147-0.01616839072240.0991777692970.286411115045-0.109347353738-0.04933478909110.1930897369620.000257704931219-0.004326378079250.142740410956-0.01133937794850.20986927239511.2915848234-3.64621145953-1.68126432656
32.811790963690.6623912353011.093298373931.99344171371.744053799767.12141579279-0.280635893233-0.1396308035870.506591590113-0.0634222204666-0.06458968672930.108283429837-0.544125965061-0.7866540286950.3626966047810.15808113157-0.001363512213670.0236224049580.1491993522560.007333510183480.17173966847911.29192465133.53038442903-1.59599027385
43.640486293563.100658060325.290576134694.931814894273.845343038629.51475720742-0.1350075976190.1453840229130.114950428687-0.4370716704490.05825757036960.181843999747-0.218419810883-0.5239875623660.06704779077820.220614059113-0.02645747397850.02306207617910.3745788200180.01415568416550.2604038606965.610290993722.46547652741-13.0521334412
58.45188891831-3.646019562144.870594585679.19351443-0.3022122094522.00286361512-0.0400095549770.369587044831-1.338687777220.01862165290120.3922282164050.0817181034811.593415053020.169669770547-0.3439876797430.345482110718-0.007771867759290.03035824619340.285219621513-0.07062913575620.52640668133810.4373427066-4.68133566752-3.6420341949
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 60 )A22 - 601 - 39
22chain 'A' and (resid 61 through 105 )A61 - 10540 - 84
33chain 'A' and (resid 106 through 122 )A106 - 12285 - 101
44chain 'A' and (resid 123 through 138 )A123 - 138102 - 117
55chain 'A' and (resid 500 through 500 )B500

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