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- PDB-1d1r: NMR SOLUTION STRUCTURE OF THE PRODUCT OF THE E. COLI YCIH GENE. -

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Basic information

Entry
Database: PDB / ID: 1d1r
TitleNMR SOLUTION STRUCTURE OF THE PRODUCT OF THE E. COLI YCIH GENE.
ComponentsHYPOTHETICAL 11.4 KD PROTEIN YCIH IN PYRF-OSMB INTERGENIC REGION
KeywordsSTRUCTURAL GENOMICS / ALPHA-BETA PLAIT / OPEN-FACED BETA SANDWICH / FERREDOXIN-LIKE FOLD
Function / homology
Function and homology information


translation reinitiation / formation of translation preinitiation complex / ribosomal small subunit binding / translation initiation factor activity / mRNA binding
Similarity search - Function
Archaeal/bacterial translation initiation factor SUI1 / SUI1-like domain / Translation Initiation Factor Eif1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YciH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsCort, J.R. / Koonin, E.V. / Bash, P.A. / Kennedy, M.A.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: A phylogenetic approach to target selection for structural genomics: solution structure of YciH.
Authors: Cort, J.R. / Koonin, E.V. / Bash, P.A. / Kennedy, M.A.
History
DepositionSep 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: HYPOTHETICAL 11.4 KD PROTEIN YCIH IN PYRF-OSMB INTERGENIC REGION


Theoretical massNumber of molelcules
Total (without water)12,4881
Polymers12,4881
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 / 25structures with the lowest energy
RepresentativeModel #4closest to the average

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Components

#1: Protein HYPOTHETICAL 11.4 KD PROTEIN YCIH IN PYRF-OSMB INTERGENIC REGION


Mass: 12488.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET-29B / Production host: Escherichia coli (E. coli) / References: UniProt: P08245

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1134D 13C-SEPARATED NOESY
1252D NOESY
1323D 15N-SEPARATED NOESY
142HMQC-J
1513D SIMULTANEOUS 15N, 13C-SEPARATED NOESY

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Sample preparation

Details
Solution-IDContents
12-3 MM YCIH U-15N,13C; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 90% H2O, 10% D2O
22-3 MM YCIH U-15N; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 90% H2O, 10% D2O
32-3 MM YCIH U-15N,13C; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 99% D2O
42-3 MM YCIH U-15N; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 99% D2O
52-3 MM YCIH; 50MM SODIUM PHOSPHATE PH 7.4; 200MM NACL; 10MM DITHIOTHREITOL; 90% H2O, 10% D2O
Sample conditionsIonic strength: 200 mM NACL, 50 mM SODIUM PHOSPHATE / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UNITYPLUSVarianUNITYPLUS7502
Varian UNITYPLUSVarianUNITYPLUS5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felix97MSIstructure solution
VNMR6.1AVARIANstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
Details: OF 358 TOTAL RESTRAINTS, 311 ARE DISTANCE RESTRAINTS AND 47 ARE DIHEDRAL ANGLE RESTRAINTS. OF THE DISTANCE RESTRAINTS, 32 ARE HYDROGEN BOND RESTRAINTS (TWO PER H-BOND), 93 ARE SEQUENTIAL, 50 ...Details: OF 358 TOTAL RESTRAINTS, 311 ARE DISTANCE RESTRAINTS AND 47 ARE DIHEDRAL ANGLE RESTRAINTS. OF THE DISTANCE RESTRAINTS, 32 ARE HYDROGEN BOND RESTRAINTS (TWO PER H-BOND), 93 ARE SEQUENTIAL, 50 ARE MEDIUM RANGE, AND 136 ARE LONG RANGE. NO INTRARESIDUE DISTANCE RESTRAINTS WERE USED.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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