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Yorodumi- PDB-2z33: Solution structure of the DNA complex of PhoB DNA-binding/transac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z33 | ||||||
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Title | Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / WINGED HELIX-TURN-HELIX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / phosphorelay response regulator activity / regulation of DNA-templated transcription initiation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing molecluar dynamics | ||||||
Authors | Yamane, T. / Okamura, H. / Ikeguchi, M. / Nishimura, Y. / Kidera, A. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment. Authors: Yamane, T. / Okamura, H. / Ikeguchi, M. / Nishimura, Y. / Kidera, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z33.cif.gz | 538.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z33.ent.gz | 447.4 KB | Display | PDB format |
PDBx/mmJSON format | 2z33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z33_validation.pdf.gz | 364.9 KB | Display | wwPDB validaton report |
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Full document | 2z33_full_validation.pdf.gz | 511.9 KB | Display | |
Data in XML | 2z33_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 2z33_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/2z33 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/2z33 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: DNA chain | Mass: 4872.190 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4921.229 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 12173.898 Da / Num. of mol.: 1 / Fragment: residues 1-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoB / Plasmid: PT7-7-CB / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFJ5 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 6.8 / Pressure: AMBIENT / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing molecluar dynamics / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2508 RESTRAINTS, 2263 ARE NOE-DERIVED DISTANCE RESTRAINTS 229 ARE DIHEDRAL ANGLE RESTRAINTS AND 16 ARE RESTRAINTS OF DNA BASE PLANALITY RESTRAINTS. ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2508 RESTRAINTS, 2263 ARE NOE-DERIVED DISTANCE RESTRAINTS 229 ARE DIHEDRAL ANGLE RESTRAINTS AND 16 ARE RESTRAINTS OF DNA BASE PLANALITY RESTRAINTS. STRUCTURE CALCULATIONS WERE PERFORMED WITH CNS BY FOLLOWIN PROCEDURE. FIRST, ONLY THE STRUCTURES OF PROTEIN WERE CALCULATED USING THE HYBRID DISTANCE GEOMETRY-SIMULATED ANNEAING PROTOCOL WITH THE INTRA-PROTEIN RESTRAINTS, 10 OUT OF 100 CALCULATED STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATION GREATER THAN 0.2 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATION GREATER THAN 2 DEGREES and A LOW TARGET ENERGY. SECOND, THE PROTEIN AND AN IDEALIZED B-FORM OF 16-MER DUPLEX DNA WERE DOCKED BY A SIMULATED ANNEALING PROTOCOL, FOR WHICH THE INTRA-DNA, INTER-MOLECULAR AND INTRA-PROTEIN RESTRAINTS WERE EMPLOYED. AS AN INITIAL STRUCTURE, EACH OF THE 10 PROTEIN STRUCTURES WAS PLACED IN 15 DIFFERENT POSITIONS 50 ANGSTROMS AWAY FROM THE DNA. NEXT, EACH OF THE 150 DOCKED COMPLEX STRUCTURES WAS FURTHER REFINED BY A SIMULATED ANNEALING PROTOCOL. FINALLY, 20 STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATION GREATER THAN 0.2 ANGSTROME AND NO TORSION ANGLE VIOLATION THAN 2 DEGREES AND A LOW TARGET ENERGY. ADDITIONALLY, 10 CNS-SELECTED STRUCTURES WERE REFINED IN REALISTIC SOLUTION SISTEM BY USING MOLECULAR DYNAMICS SIMULATION PROGRAM, MARBLE WITH RESTRAINT FUNCTIONS FOR NOE DISTANCE DIHEDRAL ANGLE AND PLANARITY OF DNA BASE PAIR USED IN CNS. | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |