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- PDB-2kl2: NMR solution structure of A2LD1 (gi:13879369) -

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Basic information

Entry
Database: PDB / ID: 2kl2
TitleNMR solution structure of A2LD1 (gi:13879369)
ComponentsAIG2-like domain-containing protein 1
KeywordsTRANSFERASE / PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / gamma-glutamylamine cyclotransferase
Function / homology
Function and homology information


gamma-glutamylamine cyclotransferase / cellular modified amino acid catabolic process / gamma-glutamylaminecyclotransferase activity / cytosol
Similarity search - Function
Gamma-glutamylaminecyclotransferase / Gamma-glutamylcyclotransferase, AIG2-like domain / Gamma-glutamyl cyclotransferase, AIG2-like / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-glutamylaminecyclotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 4
AuthorsPedrini, B. / Serrano, P. / Mohanty, B. / Geralt, M. / Herrmann, T. / Wuthrich, K. / Wilson, I. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.
Authors: Serrano, P. / Pedrini, B. / Geralt, M. / Jaudzems, K. / Mohanty, B. / Horst, R. / Herrmann, T. / Elsliger, M.A. / Wilson, I.A. / Wuthrich, K.
History
DepositionJun 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
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 8, 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: AIG2-like domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)17,0991
Polymers17,0991
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein AIG2-like domain-containing protein 1


Mass: 17099.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: a2ld1, gi-13879369 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q923B0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1115D APSY CBCA(CO)NH
1215D APSY (HA)CA(CO)NH
1314D APSY HACANH
1413D APSY (HA)CANH
1513D HNCA
1613D aliphatic 1H-13C NOESY
1713D aromatic 1H-13C NOESY
1813D 1H-15N NOESY

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Sample preparation

DetailsContents: 1.1 mM [U-100% 13C; U-100% 15N] gi-13879369, 25 mM sodium phosphate, 50 mM sodium chloride, 4.5 mM [U-100% 2H] DTT, 0.5 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMgi-13879369-1[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-21
50 mMsodium chloride-31
4.5 mMDTT-4[U-100% 2H]1
0.5 mMDTT-51
Sample conditionsIonic strength: 80.25 / pH: 6.0 / Pressure: ambient / Temperature: 298 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
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CANDIDHerrmann, Guntert and Wuthrichcollection of distance restraints
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
GAPROHiller, Fiorito, Wider Wuthrichgeometric analysis of 2d apsy projections
MATCHVolk, Herrmann, Wuthrichbackbione assignment from apsy peaks
ASCANFiorito, Herrmann, Wuthrichsidechain assignment with noesy spectra
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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