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- PDB-2lxn: Solution NMR structure of glutamine amido transferase subunit of ... -

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Basic information

Entry
Database: PDB / ID: 2lxn
TitleSolution NMR structure of glutamine amido transferase subunit of gaunosine monophosphate synthetase from Methanocaldococcus jannaschii
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsLIGASE / Glutamine amidotransferase / Ammonia channeling / De-novo purine nucleotide biosynthesis / Solution NMR structure / Methanocaldococcus jannaschii
Function / homology
Function and homology information


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding
Similarity search - Function
GMP synthase (glutamine-hydrolyzing) subunit A / GMP synthase, glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GMP synthase [glutamine-hydrolyzing] subunit A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / na
Model detailsTarget Function, model1
AuthorsAli, R. / Kumar, S. / Balaram, H. / Sarma, S.P.
CitationJournal: Biomol.Nmr Assign. / Year: 2012
Title: 1H, 13C, 15N assignment and secondary structure determination of glutamine amido transferase subunit of gaunosine monophosphate synthetase from Methanocaldococcus jannaschii
Authors: Ali, R. / Kumar, S. / Balaram, H. / Sarma, S.P.
History
DepositionAug 30, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GMP synthase [glutamine-hydrolyzing] subunit A


Theoretical massNumber of molelcules
Total (without water)21,0511
Polymers21,0511
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 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein GMP synthase [glutamine-hydrolyzing] subunit A / Glutamine amidotransferase


Mass: 21051.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: guaAA, MJ1575 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58970, GMP synthase (glutamine-hydrolysing)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1913D HNHA
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM [U-99% 15N] GATase subunit-1, 10% D2O-2, 90% H2O-3, 1mM PMSF-4, 20mM potassium phosphate-5, 0.1mM EDTA-6, 2mM DTT-7, 0.01% sodium azide-8, 90% H2O/10% D2O90% H2O/10% D2O
20.6mM [U-99% 13C; U-99% 15N] GATase subunit-9, 90% H2O-10, 10% D2O-11, 20mM potassium phosphate-12, 0.1mM EDTA-13, 2mM DTT-14, 1mM PMSF-15, 0.01% sodium azide-16, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMGATase subunit-1[U-99% 15N]1
10 %D2O-21
90 %H2O-31
1 mMPMSF-41
20 mMpotassium phosphate-51
0.1 mMEDTA-61
2 mMDTT-71
0.01 %sodium azide-81
0.6 mMGATase subunit-9[U-99% 13C; U-99% 15N]2
90 %H2O-102
10 %D2O-112
20 mMpotassium phosphate-122
0.1 mMEDTA-132
2 mMDTT-142
1 mMPMSF-152
0.01 %sodium azide-162
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
CCPNCCPNchemical shift assignment
CCPNCCPNdata analysis
CCPNCCPNpeak picking
CCPNCCPNstructure solution
Cyana-3.0Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+Cornilescu, Delaglio and Baxdata analysis
TALOS+Cornilescu, Delaglio and Baxgeometry optimization
TALOS+Cornilescu, Delaglio and Baxstructure solution
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntongeometry optimization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
ProcheckNMRLaskowski and MacArthurgeometry optimization
ProcheckNMRLaskowski and MacArthurstructure solution
CSICanadian Institutes of Health Research (CIHR Group)data analysis
CSICanadian Institutes of Health Research (CIHR Group)structure solution
MOLMOLKoradi, Billeter and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
NMR-STARHall, S. R.processing
PSVSBhattacharya and Montelionedata analysis
PSVSBhattacharya and Montelionestructure solution
PSVSBhattacharya and Montelionegeometry optimization
Cyana-3.0refinement
RefinementMethod: na / Software ordinal: 1
NMR constraintsNOE constraints total: 1781 / NOE intraresidue total count: 670 / NOE long range total count: 385 / NOE medium range total count: 200 / NOE sequential total count: 526 / Hydrogen bond constraints total count: 110 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 364 / Protein phi angle constraints total count: 178 / Protein psi angle constraints total count: 186
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 6 ° / Maximum upper distance constraint violation: 2.8 Å / Representative conformer: 1

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