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- PDB-2lg7: NMR structure of the protein YP_001302112.1 from Parabacteroides ... -

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Basic information

Entry
Database: PDB / ID: 2lg7
TitleNMR structure of the protein YP_001302112.1 from Parabacteroides Distasonis
ComponentsUncharacterized protein
KeywordsMETAL BINDING PROTEIN / APSY spectroscopy / Structural Genomics / Joint Center for Structural Genomics / JCSG / Calcium-binding protein / PSI-Biology
Function / homologyLipoxygenase-1 - #50 / PLAT/LH2 and C2-like Ca2+-binding lipoprotein / Lipoxygenase-1 / Sandwich / Mainly Beta / Peptide chain release factor 2
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsSerrano, P. / Mohanty, B. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein YP_001302112.1 from Parabacteroides Distasonis
Authors: Serrano, P. / Mohanty, B. / Geralt, M. / Wuthrich, K.
History
DepositionJul 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,8071
Polymers13,8071
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 13807.249 Da / Num. of mol.: 1 / Fragment: sequence database residues 24-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_0720 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A6L9X6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1413D 1H-15N NOESY
1515D APSY CBCA(CO)NH
1614D APSY HACANH
1715D APSY (HA)CA(CO)NH

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Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 25 mM sodium chloride, 5 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMprotein-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-21
25 mMsodium chloride-31
5 mMsodium azide-41
Sample conditionsIonic strength: 0.18 / pH: 6.0 / 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
CYANAGuntert P.refinement
CYANAGuntert P.structure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
UNIOUnio Herrmann Wuthrichpeak picking
UNIOUnio Herrmann Wuthrichchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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