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- PDB-1yh5: Solution NMR Structure of Protein yggU from Escherichia coli. Nor... -

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Basic information

Entry
Database: PDB / ID: 1yh5
TitleSolution NMR Structure of Protein yggU from Escherichia coli. Northeast Structural Genomics Consortium Target ER14.
ComponentsORF, HYPOTHETICAL PROTEIN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA+BETA / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / PSI / Protein Structure Initiative / NESG
Function / homology
Function and homology information


Conserved Hypothetical Protein Mth637; Chain: A; / YggU-like / Protein of unknown function DUF167 / YggU-like superfamily / Uncharacterised ACR, YggU family COG1872 / DUF167 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0235 protein YggU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS SIMULATED ANNEALING
AuthorsAramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Wu, M.J. / Mills, J.L. / Tejero, R.T. / Szyperski, T. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Solution Structure of the Hypothetical Protein Yggu from E. Coli. Northeast Structural Genomics Consortium Target Er14.
Authors: Aramini, J.M. / Xiao, R. / Huang, Y.J. / Acton, T.B. / Wu, M.J. / Mills, J.L. / Tejero, R.T. / Szyperski, T. / Montelione, G.T.
#1: Journal: To be Published
Title: Protein NMR Recall, Precision, and F-measure scores (RFP Scores): Structure Quality Assessment Measures Based on Information Retrieval Statistics
Authors: Huang, Y.J. / Powers, R. / Montelione, G.T.
History
DepositionJan 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF, HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,9041
Polymers11,9041
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)10 / 56structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein ORF, HYPOTHETICAL PROTEIN


Mass: 11903.733 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: YGGU / Plasmid: ER14-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PMGK / References: UniProt: Q8XCU6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-NOESY
1213D 13C-NOESY
1313D AROMATIC 13C-NOESY
1412D 15N
1511H HSQC-J
1612D 15N
1711H MEXICO
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING THE AUTOSTRUCTURE PROGRAM. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS.FINAL STRUCTURE QUALITY FACTORS FOR THE ENSEMBLE, WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 8-23,28-29,31-34,37-41,44-65,67-77,80-87: (A) RMSD FOR ORDERED RESIDUES: BB, 0.7 ANG; HEAVY ATOM, 1.2 ANG. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: 75.9%; ADDITIONALLY ALLOWED: 23.0%; GENEROUSLY ALLOWED, 1.0%; DISALLOWED, 0.2% (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): BB, -1.14/-2.23; ALL, -1.0/-4.17. (D) MAGE MOLPROBITY CLASH SCORE (RAW/Z): 33.22/-4.18 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: F-MEASURE, 0.944; RECALL, 0.977; PRECISION, 0.802; DP-SCORE, 0.726.

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Sample preparation

DetailsContents: 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5
Sample conditionsIonic strength: 50 mM NACL / pH: 6.5 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR 2.0.4 (NIH), AUTOSTRUCTURE2.0.0BRUNGER (X-PLOR), HUANG (AUTOSTRUCTURE)refinement
VNMR 6.1B6.1Bstructure solution
NMRPipe2.1structure solution
Sparky3.106structure solution
AutoAssign1.9structure solution
AutoStructure2.0.0structure solution
HYPER2.7structure solution
TALOS2.1structure solution
PdbStat3.27structure solution
XPLOR2.0.4 (NIH), PSVS 1.0structure solution
RefinementMethod: TORSION ANGLE DYNAMICS SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS PER RESIDUE; 4.1 LONG-RANGE CONTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE WITH XPLOR.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 56 / Conformers submitted total number: 10

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