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- PDB-3p7n: Crystal structure of light activated transcription factor El222 f... -

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Basic information

Entry
Database: PDB / ID: 3p7n
TitleCrystal structure of light activated transcription factor El222 from Erythrobacter litoralis
ComponentsSensor histidine kinase
KeywordsDNA BINDING PROTEIN / LOV domain / light-activated transcription factor
Function / homology
Function and homology information


nucleotide binding / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Light-activated DNA-binding protein EL222
Similarity search - Component
Biological speciesErythrobacter litoralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMcNulty, R. / Luecke, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein.
Authors: Nash, A.I. / McNulty, R. / Shillito, M.E. / Swartz, T.E. / Bogomolni, R.A. / Luecke, H. / Gardner, K.H.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Sensor histidine kinase
B: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0034
Polymers57,0902
Non-polymers9132
Water1,63991
1
A: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0022
Polymers28,5451
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0022
Polymers28,5451
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.044, 81.595, 65.478
Angle α, β, γ (deg.)90.00, 94.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sensor histidine kinase


Mass: 28545.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter litoralis (bacteria) / Strain: HTCC2594 / Gene: ELI_04755 / Plasmid: pET/100D TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2NB98
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 18.015 Da / Num. of mol.: 91 / 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

Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 8000, 0.1M MOPS pH 7.0, 0.1M ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2008
RadiationMonochromator: Bl9-1 MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→36.93 Å / Num. all: 22731 / Num. obs: 22731 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.68 % / Biso Wilson estimate: 31.79 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_417)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PR5 1YIO

2pr5

1yio


Resolution: 2.1→34.595 Å / SU ML: 0.42 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3285 1092 4.93 %Random
Rwork0.2626 ---
obs0.2659 22135 97.31 %-
all-22731 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.387 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 43.872 Å2
Baniso -1Baniso -2Baniso -3
1-17.6889 Å2-0 Å20.8317 Å2
2---11.5337 Å20 Å2
3----6.1553 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 62 91 3117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033072
X-RAY DIFFRACTIONf_angle_d0.7794168
X-RAY DIFFRACTIONf_dihedral_angle_d15.3031156
X-RAY DIFFRACTIONf_chiral_restr0.055486
X-RAY DIFFRACTIONf_plane_restr0.002526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1-2.19560.49131210.44522506262792
2.1956-2.31130.41561330.37772521265494
2.3113-2.45610.42081380.32182573271196
2.4561-2.64570.37121520.29922623277598
2.6457-2.91180.36491330.28022679281299
2.9118-3.33280.33751450.264926842829100
3.3328-4.19790.30811320.21527142846100
4.1979-34.59990.25691380.21927432881100

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