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

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Basic information

Entry
Database: PDB / ID: 4hnb
TitleCrystal Structure of Rhodobacter Sphaeroides LOV protein
ComponentsLOV proteinLight-oxygen-voltage-sensing domain
KeywordsSIGNALING PROTEIN / LOV PAS HTH / signaling
Function / homology
Function and homology information


PAS domain / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-FNR / LOV protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 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
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOV protein
B: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9774
Polymers39,0622
Non-polymers9152
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9872
Polymers19,5311
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: LOV protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9892
Polymers19,5311
Non-polymers4581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.346, 109.346, 85.479
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein LOV protein / Light-oxygen-voltage-sensing domain


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 / Gene: Rhodobacter sphaeroides / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1E1F8*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.43 %
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: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.34→38.956 Å / Num. obs: 21851 / % possible obs: 88.7 % / Redundancy: 3.6 %
Reflection shellResolution: 2.34→2.38 Å / % possible all: 93.1

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→38.956 Å
RfactorNum. reflectionSelection details
Rfree0.244 1991 random
Rwork0.204 --
obs0.2075 21827 -
Refinement stepCycle: LAST / Resolution: 2.34→38.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 62 75 2880

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