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- PDB-6gb3: A fast recovering full-length LOV protein (DsLOV) from the marine... -

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Basic information

Entry
Database: PDB / ID: 6gb3
TitleA fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - M49S mutant
ComponentsPutative blue-light photoreceptor
KeywordsSIGNALING PROTEIN / LIGHT-OXYGEN-VOLTAGE / LOV / PAS
Function / homology
Function and homology information


PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Putative blue-light photoreceptor
Similarity search - Component
Biological speciesDinoroseobacter shibae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsGranzin, J. / Batra-Safferling, R. / Roellen, K.
CitationJournal: Biochemistry / Year: 2018
Title: Mechanistic Basis of the Fast Dark Recovery of the Short LOV Protein DsLOV from Dinoroseobacter shibae.
Authors: Fettweiss, T. / Rollen, K. / Granzin, J. / Reiners, O. / Endres, S. / Drepper, T. / Willbold, D. / Jaeger, K.E. / Batra-Safferling, R. / Krauss, U.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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

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Assembly

Deposited unit
A: Putative blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2732
Polymers16,8171
Non-polymers4561
Water1,20767
1
A: Putative blue-light photoreceptor
hetero molecules

A: Putative blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5464
Polymers33,6342
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3600 Å2
ΔGint-23 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.879, 30.978, 49.477
Angle α, β, γ (deg.)90.00, 112.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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Components

#1: Protein Putative blue-light photoreceptor


Mass: 16816.803 Da / Num. of mol.: 1 / Mutation: M49S
Source method: isolated from a genetically manipulated source
Details: C-terminal hexa-histidine-tagged fusion proteins (tag sequence: LEHHHHHH) in E. coli BL21(DE3)
Source: (gene. exp.) Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12) (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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate, 1 M Ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.75→45.58 Å / Num. obs: 12224 / % possible obs: 94.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.125 / Net I/σ(I): 18.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 601 / CC1/2: 0.924 / Rrim(I) all: 0.262 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KUK

4kuk


Resolution: 1.752→45.579 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.63
RfactorNum. reflection% reflection
Rfree0.2121 632 5.17 %
Rwork0.1526 --
obs0.1558 12222 94.88 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 1.752→45.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 31 67 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051003
X-RAY DIFFRACTIONf_angle_d0.7741377
X-RAY DIFFRACTIONf_dihedral_angle_d15.631605
X-RAY DIFFRACTIONf_chiral_restr0.051154
X-RAY DIFFRACTIONf_plane_restr0.005180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7516-1.88690.24631020.16632292X-RAY DIFFRACTION95
1.8869-2.07680.2411340.14652217X-RAY DIFFRACTION91
2.0768-2.37730.22121150.14872258X-RAY DIFFRACTION93
2.3773-2.9950.21781340.16182329X-RAY DIFFRACTION96
2.995-45.59440.1911470.14852494X-RAY DIFFRACTION99

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