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- PDB-4hj4: Crystal Structure of Rhodobacter Sphaeroides LOV protein -

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Basic information

Entry
Database: PDB / ID: 4hj4
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: 2.703 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)39,9754
Polymers39,0622
Non-polymers9132
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.800, 70.500, 74.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LOV protein


Mass: 19531.078 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: M1E1G2*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.: 12 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG400, 0.15 M MgCl2, 0.1 M HEPES, pH 8.5, 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: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 9927 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.107 / Χ2: 2.31 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.755.80.3664780.824199.2
2.75-2.86.10.3794690.8921100
2.8-2.856.50.355030.7841100
2.85-2.916.80.3464780.8791100
2.91-2.9770.3374840.891100
2.97-3.047.10.2694880.9541100
3.04-3.127.20.2494961.0191100
3.12-3.27.20.2114981.0381100
3.2-3.297.20.1764721.2771100
3.29-3.47.20.1634891.2831100
3.4-3.527.20.1354931.7481100
3.52-3.667.20.1224921.9951100
3.66-3.837.20.1065002.4611100
3.83-4.037.10.0974822.8291100
4.03-4.287.10.094993.2211100
4.28-4.6170.0915024.611100
4.61-5.0770.0835153.8811100
5.07-5.870.0835023.2851100
5.8-7.36.80.0795233.8751100
7.3-306.20.0785647.6381100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.703→29.813 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8222 / SU ML: 0.24 / σ(F): 1.36 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 1025 10.37 %
Rwork0.1935 --
obs0.1997 9886 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.38 Å2 / Biso mean: 66.1312 Å2 / Biso min: 37 Å2
Refinement stepCycle: LAST / Resolution: 2.703→29.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 62 12 2801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082841
X-RAY DIFFRACTIONf_angle_d1.2343846
X-RAY DIFFRACTIONf_chiral_restr0.075405
X-RAY DIFFRACTIONf_plane_restr0.006516
X-RAY DIFFRACTIONf_dihedral_angle_d18.3431060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.703-2.84540.28511260.18921246137299
2.8454-3.02360.25541360.189612411377100
3.0236-3.25670.24531320.181612551387100
3.2567-3.5840.23531560.169712471403100
3.584-4.10150.22071560.164212561412100
4.1015-5.1630.24971470.193112801427100
5.163-29.81520.27681720.2313361508100

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