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

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Basic information

Entry
Database: PDB / ID: 6gba
TitleA fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - M49A 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: 1.9 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

Downloads & links

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Assembly

Deposited unit
A: Putative blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2572
Polymers16,8011
Non-polymers4561
Water91951
1
A: Putative blue-light photoreceptor
hetero molecules

A: Putative blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5144
Polymers33,6022
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3550 Å2
ΔGint-25 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.880, 30.931, 49.132
Angle α, β, γ (deg.)90.00, 112.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative blue-light photoreceptor


Mass: 16800.803 Da / Num. of mol.: 1 / Mutation: M49A
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)
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.: 51 / 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: 1.88 Å3/Da / Density % sol: 34.57 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl, 30 % PEG 6000

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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: 1.9→45.25 Å / Num. obs: 9733 / % possible obs: 97.5 % / Redundancy: 4 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.079 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.651 / Num. unique obs: 627 / CC1/2: 0.878 / Rrim(I) all: 0.746 / % possible all: 98.2

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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: 1.9→28.974 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.35
RfactorNum. reflection% reflection
Rfree0.2176 481 4.95 %
Rwork0.1774 --
obs0.1796 9724 96.86 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 31 51 1000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006977
X-RAY DIFFRACTIONf_angle_d0.8331338
X-RAY DIFFRACTIONf_dihedral_angle_d15.278580
X-RAY DIFFRACTIONf_chiral_restr0.054149
X-RAY DIFFRACTIONf_plane_restr0.007175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-2.04680.2678880.21971846X-RAY DIFFRACTION97
2.0468-2.25270.226850.19491858X-RAY DIFFRACTION98
2.2527-2.57860.24481050.21261828X-RAY DIFFRACTION97
2.5786-3.2480.2515830.19051784X-RAY DIFFRACTION93
3.248-28.97780.19121200.15041927X-RAY DIFFRACTION99
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)
13.67931.7753.48354.3014-0.86675.22430.128-0.21550.8116-0.12740.14520.7196-1.2394-0.1218-0.15350.48320.00470.01870.397-0.11920.565211.891610.8176-15.4832
24.33351.85392.60463.8660.39233.96150.00270.3384-0.0303-0.28150.091-0.05560.17410.306-0.09410.2444-0.00870.04660.317-0.04060.206317.43551.0341-10.2064
32.8244-0.60760.34381.1610.04722.540.0465-0.0702-0.4730.03490.02780.02930.33780.2304-0.06180.22450.02690.01820.17010.00810.239410.3665-6.4999-1.9174
42.73750.82330.14511.08610.3411.4498-0.10690.29870.1233-0.04250.07880.0469-0.09220.07080.0910.17790.0039-0.01370.2372-0.00990.20149.34661.88-1.3832
52.7605-0.28660.77822.5001-0.19235.3179-0.09730.33880.3352-0.43630.01370.40160.0023-0.35050.15480.2176-0.0648-0.01930.40710.04110.26535.40322.4698-12.7777
63.8612.24081.9877.2268-1.26342.9294-0.08730.1267-1.0667-0.7046-0.2997-0.21631.70850.30470.35340.438-0.030.08110.2892-0.1020.39310.2783-4.3137-4.4245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 94 )
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 139 )
6X-RAY DIFFRACTION6chain 'A' and (resid 500 through 500 )

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