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- PDB-5syq: Solution structure of Aquifex aeolicus Aq1974 -

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Basic information

Entry
Database: PDB / ID: 5syq
TitleSolution structure of Aquifex aeolicus Aq1974
ComponentsUncharacterized protein aq_1974
KeywordsStructural Genomics / Unknown Function / Aromatic Claw protein of unknown function highly aromatic protein / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Midwest Center for Structural Genomics / MCSG / PSI-biology
Function / homologyUncharacterised protein aq_1974-like / Uncharacterized protein aq_1974
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / na
AuthorsSachleben, J.R. / Gawlak, G. / Hoey, R.J. / Liu, G. / Joachimiak, A. / Montelione, G.T. / Koide, S. / Northeast Structural Genomics Consortium (NESG) / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2017
Title: Aromatic claw: A new fold with high aromatic content that evades structural prediction.
Authors: Sachleben, J.R. / Adhikari, A.N. / Gawlak, G. / Hoey, R.J. / Liu, G. / Joachimiak, A. / Montelione, G.T. / Sosnick, T.R. / Koide, S.
History
DepositionAug 11, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionSep 28, 2016ID: 2N0P
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_struct_assembly_auth_evidence / Item: _entity.pdbx_number_of_molecules
Revision 1.4Jun 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
Revision 1.5May 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:
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Assembly

Deposited unit
A: Uncharacterized protein aq_1974


Theoretical massNumber of molelcules
Total (without water)10,4161
Polymers10,4161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 18all calculated structures submitted
RepresentativeModel #1lowest energy
DetailsMonomer according to gel filtration

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Components

#1: Protein Uncharacterized protein aq_1974


Mass: 10415.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: aq_1974 / Plasmid: PHFT1-Aq1974 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O67784

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic13D HN(CA)CO
171isotropic13D C(CO)NH
181isotropic13D HBHA(CO)NH
191isotropic13D H(CCO)NH
1101isotropic13D (H)CCH-TOCSY
1151isotropic12D (HB)CB(CGCD)HD
1161isotropic12D (HB)CB(CGCDCE)HE
1111isotropic13D 1H-15N TOCSY
1121isotropic13D 1H-15N NOESY
1131isotropic13D 1H-13C NOESY aliphatic
1141isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 332 uM [U-100% 13C; U-100% 15N] Aq_1974, 20 mM sodium phosphate, 150 mM sodium chloride, 93% H2O/7% D2O
Label: Sample 1 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
332 uMAq_1974[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenone1
150 mMsodium chloridenone1
Sample conditionsIonic strength: 180 mM / Label: conditions 1 / pH: 7.4 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
RefinementMethod: na / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 18 / Conformers submitted total number: 18

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