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- PDB-2hpu: Solution NMR structure of the apo-NosL protein from Achromobacter... -

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Basic information

Entry
Database: PDB / ID: 2hpu
TitleSolution NMR structure of the apo-NosL protein from Achromobacter cycloclastes
ComponentsNosL protein
KeywordsMETAL TRANSPORT / alpha beta topology
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2050 / Alpha-Beta Plaits - #2060 / Nitrous oxide reductase accessory protein NosL / NosL / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Copper-binding lipoprotein NosL
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodSOLUTION NMR / Ambiguous Restraints for Iterative Assignment (ARIA 1.2),torsion angle dynamics, simulated annealing
AuthorsTaubner, L.M. / McGuirl, M.A. / Dooley, D.M. / Copie, V.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Studies of Apo Nosl, an Accessory Protein of the Nitrous Oxide Reductase System: Insights from Structural Homology with MerB, a Mercury Resistance Protein.
Authors: Taubner, L.M. / McGuirl, M.A. / Dooley, D.M. / Copie, V.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NosL protein


Theoretical massNumber of molelcules
Total (without water)18,5521
Polymers18,5521
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 / 100structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein NosL protein


Mass: 18551.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Strain: IAM1013 / Gene: nosL / Plasmid: pET-20b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O68481

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HNCO
131HN(CA)CB
141CBCA(CO)NH
151C(CO)NH
161HCC(CO)NH
1731H-13C-CT HSQC
183(H)CCH-TOCSY
1923D 15N NOESY
110215N NOESY-HSQC
111313C NOESY-HSQC
NMR detailsText: Sequential and intra-residue 1H, 15N, and 13C backbone and side-chain chemical shift assignments were extracted from a series of double and triple resonance NMR experiments (HNCA, HNCO, HNCACB, ...Text: Sequential and intra-residue 1H, 15N, and 13C backbone and side-chain chemical shift assignments were extracted from a series of double and triple resonance NMR experiments (HNCA, HNCO, HNCACB, CBCA(CO)NH, C(CO)NH, HCC(CO)NH, 1H-13C-CT HSQC,and HCCH-TOCSY) conducted on a DRX600. nOe data were obtained from 3D 15N NOESY experiments with mixing times (tmix) of 100, 120, and 140 msec and from 3D HCHC-NOESY (tmix=140 msec) spectra acquired at 600 MHz. Additional 15N NOESY-HSQC and 13C NOESY-HSQC experiments (nOe mixing times of 120 msec) were acquired on a Varian 800 INOVA (800 MHz) instrument.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM NosL, U-15N, 13C; 100mM sodium phosphate; 1mM EDTA; 1mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
21.0 mM NosL, U-15N; 100mM sodium phosphate; 1mM EDTA; 1mM DTT; 95% H2O, 5% D2O95% H2O/5% D2O
31.0 mM NosL, U-15N, 13C; 100mM sodium phosphate; 1mM EDTA; 1mM DTT; > 95% D2O> 95% D2O
Sample conditionsIonic strength: 100mM sodium phosphate / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Bruker Inc.processing
NMRPipe2.4Delaglioprocessing
NMRView5Johnsondata analysis
ARIA1.2Nilgesstructure solution
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
RefinementMethod: Ambiguous Restraints for Iterative Assignment (ARIA 1.2),torsion angle dynamics, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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