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- PDB-1x0p: Structure of a cyanobacterial BLUF protein, Tll0078 -

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Basic information

Entry
Database: PDB / ID: 1x0p
TitleStructure of a cyanobacterial BLUF protein, Tll0078
Componentshypothetical protein Tll0078Hypothesis
KeywordsELECTRON TRANSPORT / BLUF / Tll0078 / FAD / STRUCTURAL GENOMICS
Function / homology
Function and homology information


blue light photoreceptor activity / FAD binding
Similarity search - Function
Helix Hairpins - #1540 / Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Helix Hairpins / Alpha-Beta Plaits / 2-Layer Sandwich ...Helix Hairpins - #1540 / Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Helix Hairpins / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Tll0078 protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å
AuthorsKita, A. / Okajima, K. / Morimoto, Y. / Ikeuchi, M. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of a Cyanobacterial BLUF Protein, Tll0078, Containing a Novel FAD-binding Blue Light Sensor Domain
Authors: Kita, A. / Okajima, K. / Morimoto, Y. / Ikeuchi, M. / Miki, K.
History
DepositionMar 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 24, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: hypothetical protein Tll0078
B: hypothetical protein Tll0078
C: hypothetical protein Tll0078
D: hypothetical protein Tll0078
E: hypothetical protein Tll0078
F: hypothetical protein Tll0078
G: hypothetical protein Tll0078
H: hypothetical protein Tll0078
I: hypothetical protein Tll0078
J: hypothetical protein Tll0078
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,45620
Polymers165,60010
Non-polymers7,85610
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.511, 109.850, 169.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
hypothetical protein Tll0078 / Hypothesis


Mass: 16560.004 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DMN3
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.6 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG400, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2003
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 105793 / Num. obs: 105793 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 65.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SIR / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 5177 RANDOM
Rwork0.231 --
all-102412 -
obs-102412 -
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11270 0 270 276 11816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0096
X-RAY DIFFRACTIONc_angle_d1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.73

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