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- PDB-2l52: Solution structure of the small archaeal modifier protein 1 (SAMP... -

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Basic information

Entry
Database: PDB / ID: 2l52
TitleSolution structure of the small archaeal modifier protein 1 (SAMP1) from Methanosarcina acetivorans
ComponentsMETHANOSARCINA ACETIVORANS SAMP1 HOMOLOG
KeywordsPROTEIN BINDING / beta-grasp fold / SAMP1 / SAMP / E1-LIKE / SAMP-ACTIVATOR / ELSA / ADENYLATION / UBIQUITIN
Function / homology
Function and homology information


MoaD, archaeal-type / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Molybdopterin converting factor, subunit 1
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsDamberger, F.F. / Ranjan, N. / Sutter, M. / Allain, F.H.-T. / Weber-Ban, E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Solution structure and activation mechanism of ubiquitin-like small archaeal modifier proteins.
Authors: Ranjan, N. / Damberger, F.F. / Sutter, M. / Allain, F.H. / Weber-Ban, E.
History
DepositionOct 24, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: METHANOSARCINA ACETIVORANS SAMP1 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)10,7081
Polymers10,7081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein METHANOSARCINA ACETIVORANS SAMP1 HOMOLOG


Mass: 10708.403 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: moaD, MA_4086 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TIQ6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D 1H-13C NOESY
1414D APSY-HACANH
1515D APSY-CBCA(CO)NH
1615D APSY-(HA)CA(CO)NH
1715D APSY-HC(CC-TOCSY)CONH
1814D APSY-(H)CCH-COSY
1914D aromatic APSY-(H)CCH-COSY
11014D APSY-HBCB(CG)CDHD
11122D 1H-15N HSQC
11212D 15N{1H}-NOE-[15N,1H]-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] protein, 150 mM sodium chloride, 20 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 15N] protein, 150 mM sodium chloride, 20 mM sodium phosphate, 0.1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSAMP1-1[U-99% 13C; U-99% 15N]1
150 mMsodium chloride-21
20 mMsodium phosphate-31
0.1 mMEDTA-41
1 mMSAMP1-5[U-99% 15N]2
150 mMsodium chloride-62
20 mMsodium phosphate-72
0.1 mMEDTA-82
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003
Bruker AvanceBrukerAVANCE7004

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Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and KOLLMANNrefinement
CYANA3CYANA (Peter Guntert)structure solution
UNIO10(Torsten Herrmann)peak picking
UNIO10(Torsten Herrmann)structure solution
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichdata analysis
GAPRO0.9.8Sebastian Hiller & Gerhard Widerpeak picking
GAPRO0.9.8Sebastian Hiller & Gerhard Widerchemical shift assignment
TopSpin2.1Bruker Biospinprocessing
MOLMOL2.2KKoradi, Billeter and Wuthrichdata analysis
MATCHHerrmann and Wuthrichchemical shift assignment
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The ensemble of 20 CYANA lowest target function conformers was minimized in AMBER using the rna.ff99 forcefield and generalized born solvent model.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

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