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- PDB-2lrv: Assignment of E coli periplasmic protein YmgD -

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Basic information

Entry
Database: PDB / ID: 2lrv
TitleAssignment of E coli periplasmic protein YmgD
ComponentsUncharacterized protein ymgD
KeywordsUNKNOWN FUNCTION
Function / homologyYmgD protein / Uncharacterised protein YmgD / YmgD domain superfamily / YmgD protein / 10k-s Protein, Hypothetical Protein A; Chain A / outer membrane-bounded periplasmic space / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YmgD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, K. / Inouye, M. / Baum, J. / Hsu, S. / Masuda, H.
CitationJournal: To be Published
Title: Solution structure of homodimeric periplasmic protein YmgD in E. coli
Authors: Wu, K. / Masuda, H. / Hsu, S.D. / Baum, J. / Inouye, M.
History
DepositionApr 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 ymgD


Theoretical massNumber of molelcules
Total (without water)9,7371
Polymers9,7371
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein ymgD


Mass: 9737.120 Da / Num. of mol.: 1 / Fragment: UNP residues 20-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ymgD, b1171, JW5177 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P0AB46
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1413D HNCO
1513D HN(CA)CO
1613D C(CO)NH
1713D HN(CA)CB
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D CBCA(CO)NH
11113D 1H-15N NOESY
11213D 1H-15N TOCSY
11313D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.4 mM [U-99% 13C; U-99% 15N] YmgD, 90 % H2O, 10 % D2O, 100 mM Sodium acetate, 50 mM NaCl, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMYmgD-1[U-99% 13C; U-99% 15N]1
90 %H2O-21
10 %D2O-31
100 mMSodium acetate-41
50 mMNaCl-51
Sample conditionsIonic strength: 0.05 / pH: 5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NOE, Dihedral angles, RDC and symmetry restraints, explicit solvent refinement and full electrostatics
NMR constraintsNOE constraints total: 1045 / NOE intraresidue total count: 260 / NOE long range total count: 94 / NOE medium range total count: 315 / NOE sequential total count: 376
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.5 Å

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