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- PDB-7tz8: Solution NMR structure of the PBS linker polypeptide domain (frag... -

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Basic information

Entry
Database: PDB / ID: 7tz8
TitleSolution NMR structure of the PBS linker polypeptide domain (fragment 254-400) of phycobilisome linker protein ApcE from Synechocystis sp. PCC 6803 refined with NH RDCs. Northeast Structural Genomics Consortium Target SgR209C
ComponentsPhycobiliprotein ApcE
KeywordsLYASE / slr0335 / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Lyases / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Tejero, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Front Mol Biosci / Year: 2022
Title: AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.
Authors: Tejero, R. / Huang, Y.J. / Ramelot, T.A. / Montelione, G.T.
History
DepositionFeb 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phycobiliprotein ApcE


Theoretical massNumber of molelcules
Total (without water)17,8681
Polymers17,8681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Phycobiliprotein ApcE / Phycobilisome LCM core-membrane linker polypeptide / Phycobilisome core-membrane linker phycobiliprotein ApcE


Mass: 17868.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: apcE, slr0335 / Plasmid: pET21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pMGK / References: UniProt: Q55544

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 1D 1H

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Sample preparation

DetailsType: solution
Contents: 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 100 mM DTT, 0.02 % sodium azide, 1.4 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O
Label: NC sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMESnatural abundance2
100 mMsodium chloridenatural abundance2
5 mMcalcium chloridenatural abundance2
100 mMDTTnatural abundance2
0.02 %sodium azidenatural abundance2
1.4 mMprotein[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 200 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3.98.14Guntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKY1.37Lee, Westler, Bahrami, Eghbalnia, Markleychemical shift assignment
PdbStat5.21.6Tejero, Snyder, Mao, Aramini, Montelionedata analysis
NMRFAM-SPARKY1.37Lee, Westler, Bahrami, Eghbalnia, Markleypeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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