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- PDB-8a5r: Crystal structure of light-activated DNA-binding protein EL222 fr... -

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Basic information

Entry
Database: PDB / ID: 8a5r
TitleCrystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized and measured in dark.
ComponentsLight-activated DNA-binding protein EL222
KeywordsTRANSCRIPTION / Light-activated transcription factor / DNA binding protein / LOV domain
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 domain / PAS-associated, C-terminal / PAC domain profile. / 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 domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Light-activated DNA-binding protein EL222
Similarity search - Component
Biological speciesErythrobacter litoralis HTCC2594 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKoval, T. / Chaudhari, A. / Fuertes, G. / Andersson, I. / Dohnalek, J.
Funding support Czech Republic, European Union, 3items
OrganizationGrant numberCountry
Czech Academy of Sciences86652036 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447European Union
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
CitationJournal: To Be Published
Title: EL222 from Erythrobacter litoralis.
Authors: Chaudhari, A. / Koval, T. / Andersson, I. / Dohnalek, J. / Fuertes, G.
History
DepositionJun 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Light-activated DNA-binding protein EL222
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9817
Polymers23,2101
Non-polymers7716
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-29 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.810, 51.961, 81.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Light-activated DNA-binding protein EL222 / EL222 / LOV-HTH DNA-binding protein


Mass: 23210.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Oxidation of His101 to 2-oxo-histidine
Source: (gene. exp.) Erythrobacter litoralis HTCC2594 (bacteria)
Strain: HTCC2594 / Gene: ELI_04755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2NB98

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Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 21% (w/v) PEG 8000, 0.22 M MgCl2, 0.11 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 20, 2020 / Details: HELIOS optics for MetalJet
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.85→30.975 Å / Num. obs: 15648 / % possible obs: 95.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.035 / Rrim(I) all: 0.078 / Χ2: 0.92 / Net I/σ(I): 13.2
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 680 / CC1/2: 0.773 / Rpim(I) all: 0.355 / Rrim(I) all: 0.567 / Χ2: 1.59 / % possible all: 69.6

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Processing

Software
NameVersionClassification
PROTEUMdata collection
PROTEUMdata reduction
SADABSdata scaling
MOLREP11.7.02phasing
Coot0.8.9.1model building
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P7N

3p7n


Resolution: 1.85→30.975 Å / Cor.coef. Fo:Fc: 0.961 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.21528 800 5.1 %Random selection
Rwork0.15986 15608 --
all0.161 ---
obs0.1607 15608 95.316 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.041 Å2-0 Å2-0 Å2
2---0.524 Å20 Å2
3---0.482 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 47 251 1900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131786
X-RAY DIFFRACTIONr_bond_other_d0.0330.0171750
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6492451
X-RAY DIFFRACTIONr_angle_other_deg2.2891.5814050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94921.93998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55715323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6861517
X-RAY DIFFRACTIONr_chiral_restr0.080.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022052
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02384
X-RAY DIFFRACTIONr_nbd_refined0.2080.2385
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.21606
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2854
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2174
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1390.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.210
X-RAY DIFFRACTIONr_nbd_other0.1930.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.231
X-RAY DIFFRACTIONr_mcbond_it1.6761.648865
X-RAY DIFFRACTIONr_mcbond_other1.6761.647864
X-RAY DIFFRACTIONr_mcangle_it2.5282.461089
X-RAY DIFFRACTIONr_mcangle_other2.5272.461090
X-RAY DIFFRACTIONr_scbond_it2.3791.986921
X-RAY DIFFRACTIONr_scbond_other2.3761.981919
X-RAY DIFFRACTIONr_scangle_it3.7412.8631348
X-RAY DIFFRACTIONr_scangle_other3.742.8651349
X-RAY DIFFRACTIONr_lrange_it5.77920.6172117
X-RAY DIFFRACTIONr_lrange_other5.69820.1652071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.8980.262566.90.26975169.2704
1.898-1.950.327525.20.23595086.9792
1.95-2.0060.2744240.202100491.3537
2.006-2.0680.257464.50.19498093.4426
2.068-2.1360.261464.60.1895195.4981
2.136-2.210.268555.40.16596497.9808
2.21-2.2940.165484.90.15193899.2951
2.294-2.3870.215515.30.148903100
2.387-2.4930.178434.60.145882100
2.493-2.6140.199485.40.15284999.8886
2.614-2.7550.18414.80.156805100
2.755-2.9210.182415.10.146759100
2.921-3.1220.255364.80.153716100
3.122-3.3710.184486.70.15466499.8597
3.371-3.690.204345.20.126619100
3.69-4.1220.154345.80.11955599.6616
4.122-4.7530.203315.70.12751299.8162
4.753-5.8040.233224.80.178440100
5.804-8.1360.273174.60.201352100
8.136-30.9750.291940.19921496.5368

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