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- PDB-6q2z: NMR solution structure of the HVO_2922 protein from Haloferax volcanii -

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Basic information

Entry
Database: PDB / ID: 6q2z
TitleNMR solution structure of the HVO_2922 protein from Haloferax volcanii
ComponentsUPF0339 family protein
KeywordsUNKNOWN FUNCTION / conserved hypothetical protein
Function / homologyYegP-like / Domain of unknown function DUF1508 / Domain of unknown function (DUF1508) / YegP-like superfamily / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / UPF0339 family protein
Function and homology information
Biological speciesHaloferax volcanii (archaea)
MethodSOLUTION NMR / simulated annealing with torsion angle dynamics / cartesian angle dynamics / molecular dynamics
AuthorsKubatova, N. / Jonker, H.R.A. / Saxena, K. / Richter, C. / Marchfelder, A. / Schwalbe, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSPP 2002 priority program - 313752925 Germany
State of Hesse - BMRZ Germany
CitationJournal: Chembiochem / Year: 2020
Title: Solution Structure and Dynamics of the Small Protein HVO_2922 from Haloferax volcanii.
Authors: Kubatova, N. / Jonker, H.R.A. / Saxena, K. / Richter, C. / Vogel, V. / Schreiber, S. / Marchfelder, A. / Schwalbe, H.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jul 3, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0339 family protein
B: UPF0339 family protein


Theoretical massNumber of molelcules
Total (without water)13,3732
Polymers13,3732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, heteronuclear relaxation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3180 Å2
ΔGint-18 kcal/mol
Surface area6650 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0339 family protein


Mass: 6686.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: conserved hypothetical protein HVO_2922 from Haloferax volcanii
Source: (gene. exp.) Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (archaea)
Gene: HVO_2922 / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): T7-Express / References: UniProt: D4GXU1

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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
121isotropic32D 1H-13C HSQC aliphatic
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-1H TOCSY
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-15N TOCSY
171isotropic13D HNHA
181isotropic12D 1H-15N HETNOE
191isotropic12D 1H-15N T1
1101isotropic12D 1H-15N T2
1112isotropic23D HN(CA)CB
1122isotropic23D HN(COCA)CB
1132isotropic23D HNCO
1142isotropic13D (H)CC(CO)NH
1152isotropic33D (H)CCH-TOCSY
1162isotropic33D 1H-13C NOESY aliphatic
1172isotropic13D 1H-13C TOCSY aromatic
1182isotropic32D (HB)CB(CGCD)HD
1192isotropic32D (HB)CB(CGCDCE)HE

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution15.0 mM [U-15N] HVO_2922, 50 mM sodium phosphate, 100 mM sodium chloride, 3 mM DTT, 95% H2O/5% D2O15N labeled HVO_2922 protein15N95% H2O/5% D2O
solution22.0 mM [U-13C; U-15N] HVO_2922, 50 mM sodium phosphate, 100 mM sodium chloride, 3 mM DTT, 95% H2O/5% D2O13C15N labeled HVO_2922 protein13C15N95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5.0 mMHVO_2922[U-15N]1
50 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
3 mMDTTnatural abundance1
2.0 mMHVO_2922[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
3 mMDTTnatural abundance2
Sample conditionsIonic strength: 232 mM / Label: normal / pH: 7.5 / Pressure: ambient mbar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker Avance Bruker 600BrukerAvance Bruker 6006001cryoprobe
Bruker Avance Bruker 700BrukerAvance Bruker 7007002cryoprobe
Bruker Avance Bruker 800BrukerAvance Bruker 8008003cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
Sparky3.114Goddard and Knellerchemical shift assignment
Sparky3.114Goddard and Knellerpeak picking
Sparky3.114Goddard and Knellerdata analysis
TALOSNShen and Baxdata analysis
TENSOR2Dosset, Marion, Blackledgedata analysis
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA1.2 HJLinge, O'Donoghue and Nilgesrefinement
Refinement
MethodSoftware ordinalDetails
simulated annealing with torsion angle dynamics8structure determination
cartesian angle dynamics9energy minimization
molecular dynamics10refinement in water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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