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- PDB-4hj3: Crystal Structure of Rhodobacter Sphaeroides LOV protein -

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Basic information

Entry
Database: PDB / ID: 4hj3
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: 2.643 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)40,0174
Polymers39,1042
Non-polymers9132
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.784, 105.784, 83.983
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: 19552.098 Da / Num. of mol.: 2 / Mutation: A138Y
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: M1E1F9*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.: 41 / 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: 3.47 Å3/Da / Density % sol: 64.54 %
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 / Wavelength: 0.978 Å
DetectorDate: Mar 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 15765 / % possible obs: 100 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.075 / Χ2: 1.82 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.64-2.699.60.5117720.9481100
2.69-2.739.60.5037710.9551100
2.73-2.799.70.3947960.979199.9
2.79-2.849.90.3027790.9891100
2.84-2.9110.20.2477761.0361100
2.91-2.9710.20.2367771.1341100
2.97-3.0510.50.1968001.1861100
3.05-3.1310.70.167771.1411100
3.13-3.2210.90.1377871.2641100
3.22-3.3311.10.1217791.3921100
3.33-3.4411.20.1017891.571100
3.44-3.5811.30.0947811.9441100
3.58-3.7511.30.0778082.0431100
3.75-3.9411.30.0727822.3041100
3.94-4.1911.30.0637822.3321100
4.19-4.5111.30.067892.8041100
4.51-4.9711.30.0538022.5141100
4.97-5.6911.20.0547902.391100
5.69-7.1611.10.0527982.5731100
7.16-5010.60.0398304.0631100

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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: 2.643→45.806 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8078 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 1568 9.98 %
Rwork0.1909 --
obs0.1958 15712 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.93 Å2 / Biso mean: 41.2552 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: LAST / Resolution: 2.643→45.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 62 41 2844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082857
X-RAY DIFFRACTIONf_angle_d1.2533869
X-RAY DIFFRACTIONf_chiral_restr0.078405
X-RAY DIFFRACTIONf_plane_restr0.005519
X-RAY DIFFRACTIONf_dihedral_angle_d19.571065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6429-2.72820.31691430.258312721415
2.7282-2.82570.33011390.262812671406
2.8257-2.93880.30091460.248113061452
2.9388-3.07250.29781420.243812601402
3.0725-3.23450.27241470.230712781425
3.2345-3.4370.3061430.215512721415
3.437-3.70230.2371380.181712851423
3.7023-4.07470.21881390.174113031442
4.0747-4.66380.20281410.15512791420
4.6638-5.8740.20841450.178313051450
5.874-45.81270.2091450.166313171462

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