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- PDB-2k2n: Solution structure of a cyanobacterial phytochrome GAF domain in ... -

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Basic information

Entry
Database: PDB / ID: 2k2n
TitleSolution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state
ComponentsSensor protein
KeywordsTRANSFERASE / phytochrome / GAF DOMAIN / phycocyanobilin / PCB / bacteriophytochrome / cyanobacterial phytochrome / Kinase / Phosphoprotein
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / rhythmic process
Similarity search - Function
Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. ...Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / histidine kinase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodSOLUTION NMR / torsion angle molecular dynamics, internal variable dynamics
AuthorsCornilescu, C.C. / Cornilescu, G. / Ulijasz, A.T. / Vierstra, R.D. / Markley, J.L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state.
Authors: Cornilescu, G. / Ulijasz, A.T. / Cornilescu, C.C. / Markley, J.L. / Vierstra, R.D.
History
DepositionApr 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6602
Polymers19,0721
Non-polymers5891
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sensor protein / / SyB-Cph1(GAF)


Mass: 19071.775 Da / Num. of mol.: 1 / Fragment: GAF domain (UNP residues 31-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2JIZ5, histidine kinase
#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-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D C(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
21153D HNCO antiphase
21253D HCA(CO)N antiphase
1136J MODULATED 2D 1H-13C HSQC
11423D 1H-15N NOESY
11533D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7 mM [U-13C; U-15N] SyB-Cph1(GAF), 1.7 mM PHYCOCYANOBILIN, 10 mM [U-2H] Tris-DCl, 0.03 % NaN3, 93% H2O/7% D2O93% H2O/7% D2O
22 mM SyB-Cph1(GAF), 2 mM [U-15N] PHYCOCYANOBILIN, 10 mM [U-2H] Tris-DCl, 0.03 % NaN3, 93% H2O/7% D2O93% H2O/7% D2O
31 mM SyB-Cph1(GAF), 1 mM [U-13C] PHYCOCYANOBILIN, 10 mM [U-2H] Tris-DCl, 0.03 % NaN3, 100% D2O100% D2O
41 mM [U-13C; U-15N] SyB-Cph1(GAF), 1 mM PHYCOCYANOBILIN, 10 mM [U-2H] Tris-DCl, 0.03 % NaN3, 93% H2O/7% D2O93% H2O/7% D2O
51 mM [U-13C; U-15N] SyB-Cph1(GAF), 1 mM PHYCOCYANOBILIN, 10 mM [U-2H] Tris-DCl, 0.03 % NaN3, 93% H2O/7% D2O93% H2O/7% D2O
60.5 mM SyB-Cph1(GAF), 0.5 mM [U-13C] PHYCOCYANOBILIN, 10 mM [U-2H] Tris-DCl, 0.03 % NaN3, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMSyB-Cph1(GAF)[U-13C; U-15N]1
1.7 mMPHYCOCYANOBILIN1
10 mMTris-DCl[U-2H]1
0.03 %NaN31
2 mMSyB-Cph1(GAF)2
2 mMPHYCOCYANOBILIN[U-15N]2
10 mMTris-DCl[U-2H]2
0.03 %NaN32
1 mMSyB-Cph1(GAF)3
1 mMPHYCOCYANOBILIN[U-13C]3
10 mMTris-DCl[U-2H]3
0.03 %NaN33
1 mMSyB-Cph1(GAF)[U-13C; U-15N]4
1 mMPHYCOCYANOBILIN4
10 mMTris-DCl[U-2H]4
0.03 %NaN34
1 mMSyB-Cph1(GAF)[U-13C; U-15N]5
1 mMPHYCOCYANOBILIN5
10 mMTris-DCl[U-2H]5
0.03 %NaN35
0.5 mMSyB-Cph1(GAF)6
0.5 mMPHYCOCYANOBILIN[U-13C]6
10 mMTris-DCl[U-2H]6
0.03 %NaN36
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.01 8.5 ambient 298 K
20.01 8.5 ambient 306 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
PIPPGarrettpeak picking
PIPPGarrettchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: torsion angle molecular dynamics, internal variable dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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