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- PDB-1xhs: Solution NMR Structure of Protein ytfP from Escherichia coli. Nor... -

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Basic information

Entry
Database: PDB / ID: 1xhs
TitleSolution NMR Structure of Protein ytfP from Escherichia coli. Northeast Structural Genomics Consortium Target ER111.
ComponentsHypothetical UPF0131 protein ytfP
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ER111 / AUTOSTRUCTURE / Northeast Structural Genomics Consortium / NESG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Gamma-glutamylcyclotransferase, AIG2-like domain / Gamma-glutamyl cyclotransferase, AIG2-like / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-glutamylcyclotransferase family protein YtfP / Gamma-glutamylcyclotransferase family protein YtfP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Huang, Y.J. / Swapna, G.V.T. / Paranji, R.K. / Xiao, R. / Shastry, R. / Acton, T.B. / Cort, J.R. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2007
Title: Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family.
Authors: Aramini, J.M. / Huang, Y.J. / Swapna, G.V. / Cort, J.R. / Rajan, P.K. / Xiao, R. / Shastry, R. / Acton, T.B. / Liu, J. / Rost, B. / Kennedy, M.A. / Montelione, G.T.
History
DepositionSep 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_database_related.db_name / _pdbx_nmr_software.name / _software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0131 protein ytfP


Theoretical massNumber of molelcules
Total (without water)13,9531
Polymers13,9531
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 / 56LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical UPF0131 protein ytfP


Mass: 13952.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ytfP / Plasmid: ER111-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: P39323, UniProt: P0AE48*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1314D 13C- SEPARATED NOESY
141HNHA
151HIGH RESOLUTION CH-HSQC
161BACKBONE TR EXPTS
171TOCSYS
181(H)CCH COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING HYPER AND TALOS.Completeness of NMR assignments: backbone, 97%; side chain, 91%; stereospecific methyl, 100%. Final structure quality factors for the ensemble, where ordered residues [S(PHI) + S(PSI) > 1.8] comprise 1-5,9-10,17-18,23-38,41-70,76-85,88-93,101-104,106-108: (a) RMSD for ordered residues: BB, 0.7; heavy atom, 1.2. (b) Ramachandran statistics for ordered residues: most favored: 89.9%; additionally allowed: 10.1%; generously allowed, 0.0%; disallowed, 0.0% (c) Procheck scores for ordered residues (raw/Z-): BB, -0.53/-1.77; all, -0.49/-2.90. (d) MAGE Molprobity clash score (raw/Z-): 28.47/-3.36. (e) RPF scores for goodness of fit to NOESY data: F-measure, 0.916; Recall, 0.962; Precision, 0.874; DP-score, 0.791.

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Sample preparation

DetailsContents: 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C ...Contents: 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O; 1.3 MM ER111 U-13C,15N 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3,100% D2O; 1.1 MM ER111 U-15N,5% 13C 20MM NH4OAC, 5MM CACL2, 10MM DTT, 0.02% NAN3, 5% D2O, 95% H2O
Sample conditionsIonic strength: 100 mM NACL / pH: 5.5 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA8004

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Processing

Software
NameVersionClassification
AUTOSTUCTURE2.1.0refinement
X-PLOR2.0.6refinement
CNS1.1refinement
NMR software
NameVersionDeveloperClassification
AUTOSTRUCTURE 2.1.0, XPLOR-NIH 2.0.6, CNS1.1HUANG, MONTELIONE (AUTOSTRUCTURE), SCHWIETERS, CLORE (XPLOR-NIH), BRUNGER (CNS)refinement
VNMR6.1Cstructure solution
PSVS1structure solution
NMRPipe2.3structure solution
Sparky3.91structure solution
AutoAssign1.14structure solution
HYPER3.2structure solution
PdbStat3.27structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1717 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 211 DIHEDRAL ANGLE CONSTRAINTS, AND 68 HYDROGEN BOND CONSTRAINTS (17.2 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1717 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 211 DIHEDRAL ANGLE CONSTRAINTS, AND 68 HYDROGEN BOND CONSTRAINTS (17.2 CONSTRAINTS PER RESIDUE; 6.9 LONG-RANGE CONSTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR). THE 10 LOWEST ENERGY STRUCTURES WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 56 / Conformers submitted total number: 10

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