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- PDB-4kuo: A superfast recovering full-length LOV protein from the marine ph... -

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Basic information

Entry
Database: PDB / ID: 4kuo
TitleA superfast recovering full-length LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae (Photoexcited state)
Componentsblue-light photoreceptor
KeywordsSIGNALING PROTEIN / PAS domain / light-oxygen-voltage / LOV / FMN Binding
Function / homology
Function and homology information


PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RIBOFLAVIN / Putative blue-light photoreceptor
Similarity search - Component
Biological speciesDinoroseobacter shibae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCircolone, F. / Granzin, J. / Stadler, A. / Krauss, U. / Drepper, T. / Endres, S. / Knieps-Gruenhagen, E. / Wirtz, A. / Willbold, D. / Batra-Safferling, R. / Jaeger, K.-E.
CitationJournal: BMC Microbiol / Year: 2015
Title: Structure and function of a short LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae.
Authors: Endres, S. / Granzin, J. / Circolone, F. / Stadler, A. / Krauss, U. / Drepper, T. / Svensson, V. / Knieps-Grunhagen, E. / Wirtz, A. / Cousin, A. / Tielen, P. / Willbold, D. / Jaeger, K.E. / Batra-Safferling, R.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Apr 29, 2015Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2372
Polymers16,8611
Non-polymers3761
Water1,51384
1
A: blue-light photoreceptor
hetero molecules

A: blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4754
Polymers33,7222
Non-polymers7532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3460 Å2
ΔGint-18 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.780, 30.936, 49.538
Angle α, β, γ (deg.)90.00, 113.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

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Components

#1: Protein blue-light photoreceptor / light-oxygen-voltage (LOV) photoreceptor


Mass: 16860.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dinoroseobacter shibae (bacteria) / Strain: DFL 12 / Gene: Dshi_2006 / Plasmid: pBluescript-DsLOV / Production host: Escherichia coli (E. coli) / References: UniProt: A8LP63
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 35.18 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.3 M magnesium chloride, 8% PGA-LM, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2→26.138 Å / Num. obs: 8206 / % possible obs: 93.48 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 10.62 Å2 / Rsym value: 0.061 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Mean I/σ(I) obs: 10.4 / Rsym value: 0.085 / % possible all: 98.15

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KUK

4kuk


Resolution: 2→26.138 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 397 4.84 %RANDOM
Rwork0.1633 ---
obs0.1643 8205 93.47 %-
all-8205 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→26.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 27 84 999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004955
X-RAY DIFFRACTIONf_angle_d0.7661309
X-RAY DIFFRACTIONf_dihedral_angle_d14.493350
X-RAY DIFFRACTIONf_chiral_restr0.051148
X-RAY DIFFRACTIONf_plane_restr0.003170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.28930.18441360.14792698269898
2.2893-2.88370.21041360.17062715271598
2.8837-26.14020.16311250.16662395239584

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