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- PDB-4hj6: Crystal Structure of Rhodobacter Sphaeroides LOV protein -

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Basic information

Entry
Database: PDB / ID: 4hj6
TitleCrystal Structure of Rhodobacter Sphaeroides LOV protein
ComponentsLOV protein
KeywordsSIGNALING PROTEIN / LOV / PAS / HTH
Function / homology
Function and homology information


PAS domain / PAS domain / Beta-Lactamase / PAS domain / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / LOV protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCrane, B.R. / Conrad, K.S. / Bilwes, A.M.
CitationJournal: Biochemistry / Year: 2013
Title: Light-induced subunit dissociation by a light-oxygen-voltage domain photoreceptor from Rhodobacter sphaeroides.
Authors: Conrad, K.S. / Bilwes, A.M. / Crane, B.R.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 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: LOV protein
B: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2514
Polymers39,3382
Non-polymers9132
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.134, 108.134, 84.632
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein LOV protein


Mass: 19669.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17025 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1E1G1*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.63 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 4.3 M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDate: Oct 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 28665 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.079 / Χ2: 2.854 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2410.50.58514340.9891100
2.24-2.2810.80.53414151.0831100
2.28-2.3211.10.46514181.1231100
2.32-2.3711.10.44914441.1051100
2.37-2.4211.10.33914261.2371100
2.42-2.4811.30.29614201.2781100
2.48-2.5411.30.28214151.3121100
2.54-2.6111.40.25414321.3761100
2.61-2.6911.40.19914161.4931100
2.69-2.7711.40.1714451.5471100
2.77-2.8711.50.13514351.6981100
2.87-2.9911.50.11114231.8711100
2.99-3.1211.50.09814342.1321100
3.12-3.2911.40.08514372.4941100
3.29-3.4911.50.07714273.0791100
3.49-3.7611.50.0714213.6351100
3.76-4.1411.40.06314523.9821100
4.14-4.7411.40.05914494.6481100
4.74-5.9711.30.05814494.6421100
5.97-5010.60.054147316.49199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→31.216 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.771 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2006 7.03 %
Rwork0.2065 --
obs0.2079 28549 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.97 Å2 / Biso mean: 63.3684 Å2 / Biso min: 36.54 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 62 60 2867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082860
X-RAY DIFFRACTIONf_angle_d1.1613872
X-RAY DIFFRACTIONf_chiral_restr0.074407
X-RAY DIFFRACTIONf_plane_restr0.005520
X-RAY DIFFRACTIONf_dihedral_angle_d18.6761066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2550.2951420.270119052047100
2.255-2.3160.28831440.270318511995100
2.316-2.38410.30531430.270318832026100
2.3841-2.4610.30691450.26551887203299
2.461-2.54890.31591410.260718902031100
2.5489-2.65090.31161370.27319032040100
2.6509-2.77150.27871420.265218892031100
2.7715-2.91750.2771440.253118892033100
2.9175-3.10020.2721400.259918982038100
3.1002-3.33930.26911460.236118872033100
3.3393-3.67490.2061430.20218972040100
3.6749-4.20550.19321460.174619162062100
4.2055-5.29430.15841480.153419092057100
5.2943-31.21870.20871450.176719392084100

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