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- PDB-2kb2: BlrP1 BLUF -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2kb2
TitleBlrP1 BLUF
ComponentsBlrP1
KeywordsSIGNALING PROTEIN / HYDROLASE REGULATOR / BLUF / Photoreceptor / HYDROLASE
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase activity / blue light photoreceptor activity / FAD binding / metal ion binding / identical protein binding
Similarity search - Function
BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Sensors of blue-light using FAD / : / Acylphosphatase-like domain superfamily / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. ...BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Sensors of blue-light using FAD / : / Acylphosphatase-like domain superfamily / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Diguanylate phosphodiesterase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWu, Q. / Gardner, K.H.
CitationJournal: Biochemistry / Year: 2009
Title: Structure and insight into blue light-induced changes in the BlrP1 BLUF domain
Authors: Wu, Q. / Gardner, K.
History
DepositionNov 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BlrP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3812
Polymers16,9241
Non-polymers4561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein BlrP1


Mass: 16924.289 Da / Num. of mol.: 1 / Fragment: BLUF Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Species: pneumoniae / Gene: KPN78578_15680, KPN_01598 / Production host: Escherichia coli (E. coli) / References: UniProt: A6T8V8
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.1-0.7 mM [U-99% 13C; U-99% 15N] BlrP1 BLUF, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.1 mM / Component: BlrP1 BLUF / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 30 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.1Linge, O'Donoghue and Nilgeschemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
VNMRVariancollection
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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