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

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Basic information

Entry
Database: PDB / ID: 6gbv
TitleA fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - M49T 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 / PHOSPHATE ION / Putative blue-light photoreceptor
Similarity search - Component
Biological speciesDinoroseobacter shibae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_validate_close_contact
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)17,3823
Polymers16,8311
Non-polymers5512
Water1,40578
1
A: Putative blue-light photoreceptor
hetero molecules

A: Putative blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7646
Polymers33,6622
Non-polymers1,1034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4050 Å2
ΔGint-46 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.076, 31.086, 49.411
Angle α, β, γ (deg.)90.00, 112.88, 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: 16830.828 Da / Num. of mol.: 1 / Mutation: M49T
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium, 0.8 M Sodium phosphate monobasic monohydrate, 0.8 M Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.63→45.52 Å / Num. obs: 15724 / % possible obs: 98.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.072 / Net I/σ(I): 13.2
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 760 / CC1/2: 0.699 / Rrim(I) all: 0.794 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KUK

4kuk


Resolution: 1.63→26.2 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.53
RfactorNum. reflection% reflection
Rfree0.1976 783 4.98 %
Rwork0.148 --
obs0.1505 15721 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 1.63→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 36 78 1027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005981
X-RAY DIFFRACTIONf_angle_d0.7491347
X-RAY DIFFRACTIONf_dihedral_angle_d13.255581
X-RAY DIFFRACTIONf_chiral_restr0.051151
X-RAY DIFFRACTIONf_plane_restr0.006175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.73210.27831300.17842432X-RAY DIFFRACTION97
1.7321-1.86580.21861280.14852460X-RAY DIFFRACTION98
1.8658-2.05350.17931290.12072514X-RAY DIFFRACTION99
2.0535-2.35050.16861440.12292484X-RAY DIFFRACTION99
2.3505-2.96070.19151200.16262435X-RAY DIFFRACTION96
2.9607-26.20390.20511320.15312613X-RAY DIFFRACTION100

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