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- PDB-2mwg: Full-Length Solution Structure Of YtvA, a LOV-Photoreceptor Prote... -

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Basic information

Entry
Database: PDB / ID: 2mwg
TitleFull-Length Solution Structure Of YtvA, a LOV-Photoreceptor Protein and Regulator of Bacterial Stress Response
ComponentsBlue-light photoreceptor
KeywordsPROTEIN BINDING / Photoreceptor / LOV/PAS / Stressosome / Rsb
Function / homology
Function and homology information


response to stimulus / photoreceptor activity
Similarity search - Function
STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 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 ...STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Blue-light photoreceptor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / monte-carlo simulated annealing using torsion angle dynamics, simulated annealing.
AuthorsJurk, M. / Bardiaux, B. / Schmieder, P.
CitationJournal: To be Published
Title: Solution Structure of YtvA from Bacillus subtilis Provides Insight into Activation Mechanism and Regulation of Bacterial Stress Response.
Authors: Jurk, M. / Dorn, M. / Reichenwallner, J. / Bardiaux, B. / Hinderberger, D. / Schmieder, P.
History
DepositionNov 7, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Other
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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

Downloads & links

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Assembly

Deposited unit
A: Blue-light photoreceptor
B: Blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2094
Polymers58,2972
Non-polymers9132
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Blue-light photoreceptor / Photoactive flavo-yellow protein / Phototropin homolog


Mass: 29148.361 Da / Num. of mol.: 2 / Fragment: UNP residues 2-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pfyP, ytvA, BSU30340 / Plasmid: pET30EK/LIC / Production host: Escherichia coli (E. coli) / References: UniProt: O34627
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D (H)CCH-TOCSY
1223D 1H-13C NOESY aliphatic
1332D 1H-15N TROSY
1442D 1H-15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1500 uM [U-13C; U-15N; U-2H; {ILE, LEU, VAL 1H-Met}] YtvA, 500 uM [U-75% 13C; U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
2500 uM [U-15N; U-2H; {ILE, LEU, VAL 1H-Met}] YtvA, 500 uM [U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
3100 uM [U-15N; U-2H] YtvA, 100 uM [U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 10 mg/mL Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
4100 uM [U-15N; U-2H] YtvA, 100 uM [U-75% 15N; U-75% 2H] FMN, 20 mM potassium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 4 % C12E5, 1.5 % Hexanol, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMYtvA-1[U-13C; U-15N; U-2H; {ILE, LEU, VAL 1H-Met}]1
500 uMFMN-2[U-75% 13C; U-75% 15N; U-75% 2H]1
20 mMpotassium phosphate-31
50 mMsodium chloride-41
0.1 %sodium azide-51
500 uMYtvA-6[U-15N; U-2H; {ILE, LEU, VAL 1H-Met}]2
500 uMFMN-7[U-75% 15N; U-75% 2H]2
20 mMpotassium phosphate-82
50 mMsodium chloride-92
0.1 %sodium azide-102
100 uMYtvA-11[U-15N; U-2H]3
100 uMFMN-12[U-75% 15N; U-75% 2H]3
20 mMpotassium phosphate-133
50 mMsodium chloride-143
0.1 %sodium azide-153
10 mg/mLPf1 phage-163
100 uMYtvA-17[U-15N; U-2H]4
100 uMFMN-18[U-75% 15N; U-75% 2H]4
20 mMpotassium phosphate-194
50 mMsodium chloride-204
0.1 %sodium azide-214
4 %C12E5-224
1.5 %Hexanol-234
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinv2.1Bruker Biospincollection
TopSpinv2.1Bruker Biospinprocessing
CCPNv2.1.5CCPNchemical shift assignment
CCPNv2.1.5CCPNdata analysis
CCPNv2.1.5CCPNpeak picking
CS-ROSETTAv3.2Shen, Vernon, Baker and Baxstructure solution
X-PLOR NIHv2.30Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHv2.30Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHv2.30Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
RefinementMethod: monte-carlo simulated annealing using torsion angle dynamics, simulated annealing.
Software ordinal: 1
Details: OWING TO THE RELATIVELY LOW NUMBER OF RESTRAINTS TO DETERMINE THE STRUCTURE AB INITIO, STRUCTURES OF THE FOUR MAJOR SEGMENTS WERE CALCULATED USING CS-ROSETTA. 12,000 AND 2,000 STRUCTURES ...Details: OWING TO THE RELATIVELY LOW NUMBER OF RESTRAINTS TO DETERMINE THE STRUCTURE AB INITIO, STRUCTURES OF THE FOUR MAJOR SEGMENTS WERE CALCULATED USING CS-ROSETTA. 12,000 AND 2,000 STRUCTURES WERE CALCULATED FOR LOV OR STAS AND NCAP OR JA, RESPECTIVELY. THE LOWEST ENERGY STRUCTURE WAS FURTHER USED. THE STRUCTURES OF THE FOUR SEGMENTS OBTAINED BY CS-ROSETTA WERE REFINED AGAINST THE RDCS USING LOW TEMPERATURE SA. 100 STRUCTURES WERE CALCULATED AND THE CLOSEST TO AN AVERAGE OF THE 10 LOWEST ENERGY STRUCTURES WAS USED IN THE NEXT STEP. ALL FOUR SEGMENTS (NCAP, LOV, JA, STAS) WERE COMBINED TO A DIMERIC FULL-LENGTH STRUCTURE. THE YF1 STRUCTURE (PDB 4GCZ) WAS USED AS A TEMPLATE FOR THE ALIGNMENT OF LOV AND NCAP IN THE DIMER. ALL FOUR SEGMENTS WERE TREATED AS RIGID BODIES IN A HIGH TEMPERATURE SIMULATED ANNEALING. 100 STRUCTURES WERE CALCULATED AND THE CLOSEST TO AN AVERAGE OF THE LOWEST 10 WAS USED IN THE LAST REFINEMENT STEP. THE FINAL STRUCTURAL ENSEMBLE WAS OBTAINED USING THE SAME REFINEMENT PROTOCOLS AS IN STEP 2. 100 STRUCTURES WERE CALCULATED AND THE LOWEST 10 ARE SUBMITTED.
NMR constraintsNOE constraints total: 1192 / NOE intraresidue total count: 58 / NOE long range total count: 294 / NOE medium range total count: 380 / NOE sequential total count: 452 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 412 / Protein psi angle constraints total count: 402
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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