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Yorodumi- PDB-2cd1: Refinement of P4 stemloop structure using residual dipolar coupli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cd1 | ||||||||||||||||||||
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Title | Refinement of P4 stemloop structure using residual dipolar coupling data | ||||||||||||||||||||
Components | 5'-R(*Keywords | NUCLEIC ACID / METAL BINDING SITE / P4 STEM / RIBONUCLEASE P / RIBONUCLEIC ACID / RIBOZYME / TRANSFER RNA PROCESSING | Function / homology | RNA / RNA (> 10) | Function and homology information Biological species | ESCHERICHIA COLI (E. coli) | Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS | Model type details | MINIMIZED AVERAGE | Authors | Schmitz, M. | History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cd1.cif.gz | 25.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cd1.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cd1 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cd1 | HTTPS FTP |
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-Related structure data
Related structure data | 1f6xC 1f6zC 1f78C 1f79C 1f7fC 1f7gC 1f7hC 1f7iC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 8633.143 Da / Num. of mol.: 1 / Fragment: P4 STEM, RESIDUES 1-27 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) |
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Sequence details | THE SEQUENCE CORRESPONDS TO NUCLEOTIDES 66 TO 73, AND 354 TO 360 OF THE E. COLI RNASE P RNA, WITH ...THE SEQUENCE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 1H-15N HSQC |
NMR details | Text: THE STRUCTURE WAS DETERMINED USING CONSTRAINT DATA FROM HOMONUCLEAR NMR SPECTROSCOPY AS DESCRIBED IN ENTRY 1F6X, AND ADDITIONAL RESIDUAL DIPOLAR COUPLINS FOR THE IMINO RESONANCES DERIVED FROM ...Text: THE STRUCTURE WAS DETERMINED USING CONSTRAINT DATA FROM HOMONUCLEAR NMR SPECTROSCOPY AS DESCRIBED IN ENTRY 1F6X, AND ADDITIONAL RESIDUAL DIPOLAR COUPLINS FOR THE IMINO RESONANCES DERIVED FROM HSCQ TYPE EXPERIMENTS ACQUIRED IN THE PRESENCE AND ABSENCE OF 22 MG PER ML PF1 PHAGE |
-Sample preparation
Details | Contents: 90% WATER/10% D2O |
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Sample conditions | Ionic strength: 100 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 288.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 Details: DETAILS OF THE REFINEMENT PROCEDURE AGAINST RESIDUAL DIPOLAR COUPLINGS ARE GIVEN IN THE PRIMARY REFERENCE CITATION ABOVE | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 1 |