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- PDB-2l1t: Solution Structure of the N-terminal Domain of NP_954075.1 -

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Basic information

Entry
Database: PDB / ID: 2l1t
TitleSolution Structure of the N-terminal Domain of NP_954075.1
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / putative c-di-GMP binding / GSU3033 / PilZ / PSI-Biology / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


cyclic-di-GMP binding
Similarity search - Function
Pnp Oxidase; Chain A - #70 / N-terminal PilZ-like domain / N-terminal PilZ-like domain PilZN1 / PilZ domain / PilZ domain / Pnp Oxidase; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesGeobacter sulfurreducens (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 17
AuthorsSusac, L. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein NP_954075.1 from Geobacter sulfurreducens
Authors: Susac, L. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionAug 5, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,0451
Polymers12,0451
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 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein


Mass: 12045.441 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: GSU3033 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q748G9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY (ali)
1314D APSY-HACANH
1415D APSY-HACA(CO)NH
1515D APSY-CBCA(CO)NH
1612D 1H-15N HSQC
1713D 1H-13C NOESY (aro)

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Sample preparation

DetailsContents: 0.9 mM [U-95% 13C; U-95% 15N] NP_954075.1, 25 mM sodium phosphate, 4.5 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMNP_954075.1-1[U-95% 13C; U-95% 15N]1
25 mMsodium phosphate-21
4.5 mMsodium azide-31
Sample conditionsIonic strength: 0.075 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
UNIOHermann and Wuthrichchemical shift assignment
UNIOHermann and Wuthrichpeak picking
UNIOHermann and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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