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- PDB-2lnj: Solution Structure of Cyanobacterial PsbP (CyanoP) from Synechocy... -

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Basic information

Entry
Database: PDB / ID: 2lnj
TitleSolution Structure of Cyanobacterial PsbP (CyanoP) from Synechocystis sp. PCC 6803
ComponentsPutative uncharacterized protein sll1418
KeywordsPHOTOSYNTHESIS / CyanoP / Photosystem II / PsbP / sll1418
Function / homology
Function and homology information


photosystem II oxygen evolving complex / extrinsic component of membrane / photosynthesis / calcium ion binding
Similarity search - Function
PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Mog1/PsbP, alpha/beta/alpha sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsJackson, S.A. / Hinds, M.G. / Eaton-Rye, J.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Solution structure of CyanoP from Synechocystis sp. PCC 6803: New insights on the structural basis for functional specialization amongst PsbP family proteins
Authors: Jackson, S.A. / Hinds, M.G. / Eaton-Rye, J.J.
History
DepositionDec 28, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Putative uncharacterized protein sll1418


Theoretical massNumber of molelcules
Total (without water)18,7451
Polymers18,7451
Non-polymers00
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 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative uncharacterized protein sll1418 / Sll1418 protein


Mass: 18744.592 Da / Num. of mol.: 1 / Fragment: UNP residues 24-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: psbP, sll1418, SYNGTS_1443 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73952

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY
1223D HNCA
1323D HN(CA)CB
1423D HNCO
1523D HN(CO)CA
1623D (H)CCH-TOCSY
1723D HBHA(CO)NH
1812D 1H-15N HSQC
1913D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N] PsbP-1, 5 mM TCEP-2, 25 mM sodium phosphate-3, 10 mM sodium chloride-4, 95% H2O/5% D2O95% H2O/5% D2O
20.4 mM [U-100% 13C; U-100% 15N] PsbP-5, 5 mM TCEP-6, 25 mM sodium phosphate-7, 10 mM sodium chloride-8, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMPsbP-1[U-100% 15N]1
5 mMTCEP-21
25 mMsodium phosphate-31
10 mMsodium chloride-41
0.4 mMPsbP-5[U-100% 13C; U-100% 15N]2
5 mMTCEP-62
25 mMsodium phosphate-72
10 mMsodium chloride-82
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
CCPNMR-Analysis_v2.1CCPNdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+Cornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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