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- PDB-2kmm: Solution NMR structure of the TGS domain of PG1808 from Porphyrom... -

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Basic information

Entry
Database: PDB / ID: 2kmm
TitleSolution NMR structure of the TGS domain of PG1808 from Porphyromonas gingivalis. Northeast Structural Genomics Consortium Target PgR122A (418-481)
ComponentsGuanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase
KeywordsHYDROLASE / Methods development / TGS domain / predominantly beta-sheet structure / Porphyromonas gingivalis / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


guanosine tetraphosphate metabolic process / hydrolase activity
Similarity search - Function
RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain / TGS / TGS-like ...RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain / TGS / TGS-like / Beta-grasp domain / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Cort, J.R. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Yang, Y. / Ramelot, T.A. / Cort, J.R. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the TGS domain of PG1808 from Porphyromonas gingivalis. Northeast Structural Genomics Consortium Target PgR122A (418-481)
Authors: Yang, Y. / Ramelot, T.A. / Cort, J.R. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Swapna, G. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJul 31, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase


Theoretical massNumber of molelcules
Total (without water)8,1231
Polymers8,1231
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 / 150structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase


Mass: 8123.245 Da / Num. of mol.: 1 / Fragment: sequence database residues 418-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: PG1808, PG_1808, spoT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q7MAV5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: TGS domain of PG1808 from Porphyromonas gingivalis
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D HN(CO)CA
11113D HBHA(CO)NH
11213D H(CCO)NH
11313D C(CO)NH
11413D (H)CCH-TOCSY
11513D (H)CCH-COSY
11633D (H)CCH-TOCSY
11734D CC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] TGS domain of PG1808, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-5% 13C; U-100% 15N] TGS domain of PG1808, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM [U-100% 13C; U-100% 15N] TGS domain of PG1808, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMTGS domain of PG1808-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
0.9 mMTGS domain of PG1808-7[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
1.2 mMTGS domain of PG1808-13[U-100% 13C; U-100% 15N]3
20 mMammonium acetate-143
200 mMsodium chloride-153
5 mMcalcium chloride-163
10 mMDTT-173
0.02 %sodium azide-183
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-nih-2.20 with HBDB
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 20

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