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- PDB-6bhn: Red Light-Absorbing State of NpR6012g4, a Red/Green Cyanobacterio... -

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Basic information

Entry
Database: PDB / ID: 6bhn
TitleRed Light-Absorbing State of NpR6012g4, a Red/Green Cyanobacteriochrome
ComponentsMethyl-accepting chemotaxis sensory transducer with phytochrome sensor
KeywordsSIGNALING PROTEIN / CBCR / phytochrome / bilin / cyanobacteria
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / membrane
Similarity search - Function
Chemotaxis methyl-accepting receptor / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP domain profile. / HAMP domain ...Chemotaxis methyl-accepting receptor / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP domain profile. / HAMP domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / Methyl-accepting chemotaxis sensory transducer with phytochrome sensor
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsYu, Q. / Lim, S. / Rockwell, N.C. / Martin, S.S. / Lagarias, J.C. / Ames, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)BES DE-FG02-09ER16117 United States
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Correlating structural and photochemical heterogeneity in cyanobacteriochrome NpR6012g4.
Authors: Lim, S. / Yu, Q. / Gottlieb, S.M. / Chang, C.W. / Rockwell, N.C. / Martin, S.S. / Madsen, D. / Lagarias, J.C. / Larsen, D.S. / Ames, J.B.
#1: Journal: Biomol NMR Assign / Year: 2016
Title: 1H, 15N, and 13C chemical shift assignments of cyanobacteriochrome NpR6012g4 in the red-absorbing dark state.
Authors: Yu, Q. / Lim, S. / Rockwell, N.C. / Martin, S.S. / Lagarias, J.C. / Ames, J.B.
History
DepositionOct 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis sensory transducer with phytochrome sensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9902
Polymers20,4021
Non-polymers5891
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Methyl-accepting chemotaxis sensory transducer with phytochrome sensor


Mass: 20401.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (bacteria)
Strain: ATCC 29133 / PCC 73102 / Gene: Npun_R6012 / Production host: Escherichia coli (E. coli) / References: UniProt: B2IU14
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D HNCO
132isotropic13D HNCA
142isotropic13D HN(CA)CB
152isotropic13D CBCA(CO)NH
162isotropic13D HN(CA)CO
172isotropic13D HBHA(CO)NH
181isotropic13D TOCSY-HSQC
191isotropic13D 15N NOESY-HSQC
1102isotropic13D (H)CCH-TOCSY
1113anisotropic12D IPAP-HSQC
1122isotropic12D 1H-13C HSQC aliphatic
1132isotropic12D (HB)CB(CGCD)HD
1142isotropic12D (HB)CB(CGCDCE)HE
1152isotropic13D 13C-NOESY-HSQC
1162isotropic13D 13C,15N Filtered/Edited NOESY-HSQC
1172isotropic13D 13C,15N Filtered/Edited HSQC-NOESY
1182isotropic12D Filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM N.A. sodium phosphate, 95% H2O/5% D2O15N sample95% H2O/5% D2O
solution220 mM N.A. sodium phosphate, 95% H2O/5% D2O15N13C sample95% H2O/5% D2O
filamentous virus320 mM N.A. potassium phosphate, 12 mM N.A. Pf1 phage, 95% H2O/5% D2O15N sample with phage95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphateN.A.1
20 mMsodium phosphateN.A.2
20 mMpotassium phosphateN.A.3
12 mMPf1 phageN.A.3
Sample conditionsIonic strength: 49 mM / Label: condition 1 / pH: 7.4 / Pressure: 1013 mbar / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.44SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORErefinement
NMRPipe8.9structure solution
Sparky3.12structure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: EXPLICIT WATER REFINEMENT
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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