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- PDB-2m1c: HADDOCK structure of GtYybT PAS Homodimer -

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Basic information

Entry
Database: PDB / ID: 2m1c
TitleHADDOCK structure of GtYybT PAS Homodimer
ComponentsDHH subfamily 1 protein
KeywordsHYDROLASE / PAS domain / YybT / ligand binding
Function / homology
Function and homology information


cyclic-di-AMP phosphodiesterase / cyclic-di-AMP phosphodiesterase activity / nucleic acid binding / hydrolase activity / metal ion binding / plasma membrane
Similarity search - Function
Cyclic-di-AMP phosphodiesterase GdpP/PdeA / : / Cyclic-di-AMP phosphodiesterase GdpP-like, PAS domain / : / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / diguanylate cyclase ...Cyclic-di-AMP phosphodiesterase GdpP/PdeA / : / Cyclic-di-AMP phosphodiesterase GdpP-like, PAS domain / : / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclic-di-AMP phosphodiesterase GdpP
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodSOLUTION NMR
Model detailstop 4 structures from haddock webserver, model1
AuthorsLiang, Z.X. / Pervushin, K. / Tan, E. / Rao, F. / Pasunooti, S. / Soehano, I. / Lescar, J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Solution Structure of the PAS Domain of a Thermophilic YybT Protein Homolog Reveals a Potential Ligand-binding Site.
Authors: Tan, E. / Rao, F. / Pasunooti, S. / Pham, T.H. / Soehano, I. / Turner, M.S. / Liew, C.W. / Lescar, J. / Pervushin, K. / Liang, Z.X.
History
DepositionNov 25, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 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: DHH subfamily 1 protein
B: DHH subfamily 1 protein


Theoretical massNumber of molelcules
Total (without water)26,4192
Polymers26,4192
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)4 / 200Top 4 structures from HADDOCK webserver
RepresentativeModel #1top 4 structures from haddock webserver

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Components

#1: Protein DHH subfamily 1 protein


Mass: 13209.331 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Strain: NG80-2 / Gene: DHH subfamily 1, GTNG_3419 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4ITV2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N TROSY-HSQC
1212D 13C HMQC
1313D HNCA
1413D HN(CO)CA
1513D HNCO
1613D HN(CA)CO
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D 15N-separated NOESY
11013D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.7 mM [U-99% 13C; U-99% 15N] PAS domain of DHH subfamily 1 protein, 50mM phosphate buffer NA; 95% H2O, 5% D2O, pH 6.5, 200mM NaCl, 1x protease inhibitor
Solvent system: 50mM phosphate buffer NA; 95% H2O, 5% D2O, pH 6.5, 200mM NaCl, 1x protease inhibitor
SampleConc.: 0.7 mM / Component: PAS domain of DHH subfamily 1 protein-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 50mM NaP, pH 6.5, 200mM NaCl / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIBrukerAVANCE II7002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A.T. et.al.refinement
HADDOCKAlexandre Bonvinrefinement
RefinementSoftware ordinal: 1 / Details: H2O SOLVATED DOCKING
NMR constraintsHydrogen bond constraints total count: 112
NMR representativeSelection criteria: top 4 structures from haddock webserver
NMR ensembleConformer selection criteria: Top 4 structures from HADDOCK webserver
Conformers calculated total number: 200 / Conformers submitted total number: 4

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