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- PDB-2jn0: Solution NMR structure of the ygdR protein from Escherichia coli.... -

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Basic information

Entry
Database: PDB / ID: 2jn0
TitleSolution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A.
ComponentsHypothetical lipoprotein ygdR
KeywordsMEMBRANE PROTEIN / solution NMR structure / Hypothetical Lipoprotein / PSI-2 target / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / Protein of unknown function DUF903 / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Uncharacterized lipoprotein YgdR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsRossi, P. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J.C. / Baran, M. / Swapna, G.V.T. / Acton, T.B. ...Rossi, P. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J.C. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the ygdR protein from Escherichia coli. Northeast Structural Genomics target ER382A.
Authors: Rossi, P. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.selection_criteria ..._pdbx_database_status.status_code_cs / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 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 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical lipoprotein ygdR


Theoretical massNumber of molelcules
Total (without water)7,0521
Polymers7,0521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical lipoprotein ygdR


Mass: 7051.722 Da / Num. of mol.: 1 / Fragment: Hypothetical lipoprotein ygdR, residues 2-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygdR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P65294

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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
1313D HNCO
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY
1913D HN(COCA)CB
11013D (H)CCH-COSY
11113D CCH-TOCSY
NMR detailsText: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. MONOMER IN SOLUTION BY NMR TC = 8.2 +/- 1.0 NS (1D T1/T1RHO +/- FIT STD). POSSIBLE CIS PEPTIDE RES. 20K-21P. COULD NOT BE ANAMBIGUOSLY ...Text: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. MONOMER IN SOLUTION BY NMR TC = 8.2 +/- 1.0 NS (1D T1/T1RHO +/- FIT STD). POSSIBLE CIS PEPTIDE RES. 20K-21P. COULD NOT BE ANAMBIGUOSLY ESTABLISHED DUE TO SPECTRAL OVERLAP. COORDINATES REPORTED FROM RESIDUE 4 TO 53 SECTION BASED ON ORDER PARAMETER. MANUAL RESONANCE ASSIGNMENT. 13C AND 15N EDITED NOESY WERE WERE ASSIGNED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS DETERMINED BY HYPER AND TALOS. ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 80.4%, SIDECHAIN 77.7%, AROMATIC (SC) 100%, VL METHYL STEREOSP. 80%. STRUCTURE QUALITY FACTOR PSVS 1.3: ORDERED RESIDUES RANGES B-STRAND (14-16, 6-9, 47-49, 22-24, 29-33, 39-43, 65, 50-51, 56-57) [S(PHI)+S(PSI)]>1.8. RMSD 0.6 BB, 1.1 ALL HEAVY ATOMS. RAMA: 84.1% MOST FAV, 13.6% ADDTL.ALL.,2.2% GEN. ALL.,0.1% DISALL. PROCHECK (PSI-PHI): 0.75/-2.64 (RAW/Z), PROCHECK (ALL): -0.6/-3.55 (RAW/Z), MOLPROBITY CLASH: 23.61/- 2.53 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.925, PRECISION: 0.916, F-MEASURE: 0.921, DP-SCORE: 0.731. MONOMER BY LIGHT SCATTERING

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Sample preparation

DetailsContents: 1.17 mM [U-100% 13C; U-100% 15N] ER382A, 10 mM DTT, 5 mM CaCl2, 0.1 M NaCl, 20 mM MES, 0.02 % sodium azide
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.17 mMER382A[U-100% 13C; U-100% 15N]1
10 mMDTT1
5 mMCaCl21
0.1 MNaCl1
20 mMMES1
0.02 %sodium azide1
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSSOLVE1.1BRUNGER, et. al.refinement
X-PLOR2.11.2CLORE et. al.refinement
PROCHECK NMR3.51LASKOWSKI, MACARTHURrefinement
MolProbity3.01LOVELL, RICHARDSON ET. AL.refinement
QUEEN1.1NABUURS, VUISTERrefinement
PSVS1.3BHATTACHARYA, MONTELIONErefinement
AutoStructure2.1.1structure solution
NMRPipestructure solution
Sparkystructure solution
MOLMOLstructure solution
CNSstructure solution
PROCHECKstructure solution
XPLOR-NIHstructure solution
DIANAstructure solution
QUEEN1.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NOESY ASSIGNMENT MADE WITH ITERATIVE METHOD USING CNS, HYPER (DIHEDRAL) AND DYANA FOLLOWED BY NIH- XPLOR FOR SIMMULATED ANNEALING MD. CONVERGED STRUCTURES WERE FURTHER MINIMIZED USING CNS IN ...Details: NOESY ASSIGNMENT MADE WITH ITERATIVE METHOD USING CNS, HYPER (DIHEDRAL) AND DYANA FOLLOWED BY NIH- XPLOR FOR SIMMULATED ANNEALING MD. CONVERGED STRUCTURES WERE FURTHER MINIMIZED USING CNS IN EXPLICIT H2O SHELL (NILGES PROTOCOL). FULL LENGTH SEQUENCE WAS CARRIED THROUGH THE REFINEMENT PROTOCOL. COORDINATES FROM DISORDERED REGIONS, INCLUDING HEXHIS TAG, WERE NOT REPORTED. STRUCTURE IS BASED ON 439 CONSTRAINTS (216 LONG RANGE), 43 DIHEDRAL AND 20 H-BOND.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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