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- PDB-2l32: solution structure of ubiquitin-like small archaeal modifier prot... -

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Basic information

Entry
Database: PDB / ID: 2l32
Titlesolution structure of ubiquitin-like small archaeal modifier protein in Haloferax volcanii
ComponentsSmall archaeal modifier protein 2
KeywordsPROTEIN BINDING / Ubiquitin-like small archaeal modifier proteins
Function / homology
Function and homology information


protein modification by small protein conjugation / protein tag activity / nucleotide binding
Similarity search - Function
Factor Xa Inhibitor - #50 / : / : / : / Small archaeal modifier protein 2 / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Factor Xa Inhibitor / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Small archaeal modifier protein 2
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, W. / Fan, K. / Liao, S. / Tu, X.
CitationJournal: To be Published
Title: solution structure of ubiquitin-like small archaeal modifier protein in Haloferax volcanii
Authors: Fan, S. / Zhang, W. / Liao, S. / Tu, X.
History
DepositionSep 1, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small archaeal modifier protein 2


Theoretical massNumber of molelcules
Total (without water)8,1961
Polymers8,1961
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Small archaeal modifier protein 2 / SAMP 2 / Ubiquitin-like small archaeal modifier protein 2


Mass: 8196.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (archaea) / Strain: DS2 / Gene: HVO_0202 / Production host: Escherichia coli (E. coli) / References: UniProt: D4GZE7

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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 CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D HN(CO)CA
1813D H(CCO)NH
1913D 1H-15N NOESY
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 % D2O-3, 90% H2O/10% D2O90% H2O/10% D2O
225 mM sodium phosphate-4, 100 mM sodium chloride-5, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMsodium phosphate-11
100 mMsodium chloride-21
10 %D2O-31
25 mMsodium phosphate-42
100 mMsodium chloride-52
Sample conditionsIonic strength: 0.12 / pH: 6.7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readchemical shift calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 3

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