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- PDB-5lam: Refined 3D NMR structure of the cytoplasmic rhodanese domain of t... -

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Basic information

Entry
Database: PDB / ID: 5lam
TitleRefined 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli
ComponentsInner membrane protein YgaP
KeywordsMEMBRANE PROTEIN / Rhodanese domain of YgaP / PROTEIN
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate-cyanide sulfurtransferase activity / plasma membrane
Similarity search - Function
Inner membrane protein YgaP-like, transmembrane domain / Inner membrane protein YgaP-like, transmembrane domain / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiosulfate sulfurtransferase YgaP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Energy refinement
AuthorsEichmann, C. / Tzitzilonis, C. / Nakamura, T. / Maslennikov, I. / Kwiatkowski, W. / Choe, S. / Lipton, S.A. / Guntert, P. / Riek, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of HealthR21 NS080799 United States
National Institutes of HealthP01 HD29587 United States
National Institutes of HealthR01 NS086890 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein.
Authors: Eichmann, C. / Tzitzilonis, C. / Nakamura, T. / Kwiatkowski, W. / Maslennikov, I. / Choe, S. / Lipton, S.A. / Riek, R.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Experimental preparation
Category: atom_site / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner membrane protein YgaP


Theoretical massNumber of molelcules
Total (without water)11,7161
Polymers11,7161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6670 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Inner membrane protein YgaP


Mass: 11716.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ygaP, b2668, JW2643 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS Star / References: UniProt: P55734

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1NOESY
121isotropic1TROSY
131isotropic13D 1H-15N TOCSY
141isotropic13D (H)CCH-TOCSY
151isotropic13D HN(CA)CB
161isotropic13D HN(CO)CA

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] Rhodanese domain, 95% H2O/5% D2O
Label: Rhodanese / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: Rhodanese domain / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0 mM / Label: Rhodanese / pH: 7 / Pressure: AMBIENT Pa / Temperature: 303.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
OPAL3.97Luginbuhl, Guntert, Billeter and Wuthrichrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
XEASYBartels et al.chemical shift assignment
RefinementMethod: Energy refinement / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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