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- PDB-7tzd: Solution NMR of the specialized apo-acyl carrier protein (RPA2022... -

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Basic information

Entry
Database: PDB / ID: 7tzd
TitleSolution NMR of the specialized apo-acyl carrier protein (RPA2022) from Rhodopseudomonas palustris, refined without RDCs. Northeast Structural Genomics Consortium Target RpR324
ComponentsSpecialized acyl carrier protein
KeywordsTRANSFERASE / Acp-XL / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / membrane / cytosol
Similarity search - Function
Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein AcpXL
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
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: Specialized acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)11,3101
Polymers11,3101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
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 Specialized acyl carrier protein


Mass: 11309.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA2022 / Plasmid: pET21-23C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 pMGK / References: UniProt: Q6N882

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Experimental details

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Experiment

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

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Sample preparation

DetailsType: solution
Contents: 20 mM MES, 200 mM NaCl, 5 mM CaCl, 0.02 % NaN3, 10 mM DTT, 5 uM DSS, 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 abundance1
200 mMNaClnatural abundance1
5 mMCaClnatural abundance1
0.02 %NaN3natural abundance1
10 mMDTTnatural abundance1
5 uMDSSnatural abundance1
1.4 mMprotein[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 200 mM / Label: 1 / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 1

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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
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
PdbStat5.2Tejero, Snyder, Mao, Aramini, Montelionedata analysis
NMRFAM-SPARKY3.19Lee, Westler, Bahrami, Eghbalnia, Markleypeak picking
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Refinement
MethodSoftware ordinalDetails
simulated annealing2from constraints
simulated annealing5CNS 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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