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Yorodumi- PDB-1gcc: SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gcc | ||||||
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Title | SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / PROTEIN-DNA COMPLEX / ETHYLENE INDUCIBLE / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information phloem or xylem histogenesis / ethylene-activated signaling pathway / response to nematode / defense response / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING PROTOCOL IN X-PLOR 3.1 WAS CARRIED OUT TO OBTAIN 25 STRUCTURES. MINIMIZED MEAN STRUCTURE OF THEM WAS FURTHER REVISED BY A 300 PS RESTRAINED MOLECULAR DYNAMICAL CALCULATION IN THE PRESENCE OF APPROXIMATELY 5000 TIP3P WATER MOLSCULES, USING CORNELL FORCE FIELD IN AMBER 4.1. THE MEAN CO-ORDINATE OF 200 STRUCTURES OBTAINED AFTER THE EQUILIBRIUM (100 PS) WAS ENERGY-MINIMIZED. | ||||||
Authors | Yamasaki, K. / Allen, M.D. / Ohme-Takagi, M. / Tateno, M. / Suzuki, M. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. Authors: Allen, M.D. / Yamasaki, K. / Ohme-Takagi, M. / Tateno, M. / Suzuki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gcc.cif.gz | 43.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gcc.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gcc_validation.pdf.gz | 254.9 KB | Display | wwPDB validaton report |
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Full document | 1gcc_full_validation.pdf.gz | 254.7 KB | Display | |
Data in XML | 1gcc_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 1gcc_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gcc ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gcc | HTTPS FTP |
-Related 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: 3319.175 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3390.209 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 7247.318 Da / Num. of mol.: 1 / Fragment: GCC-BOX BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: DNA-BINDING DOMAIN OF ATERF1; / Cell line: BL21 / Gene: ATERF1 / Plasmid: PAF104 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O80337 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: SIGNALS DUE TO PROTEINS WERE OBTAINED BY NOESY, TOCSY, DQF-COSY FOR UNLABELED SAMPLE AND 1H-15N HSQC, 3D 1H-15N NOESY-HMQC AND 3D 1H-15N TOCSY-HMQC FOR THE SAMPLE WITH 15N-LABELED PROTEIN. ...Text: SIGNALS DUE TO PROTEINS WERE OBTAINED BY NOESY, TOCSY, DQF-COSY FOR UNLABELED SAMPLE AND 1H-15N HSQC, 3D 1H-15N NOESY-HMQC AND 3D 1H-15N TOCSY-HMQC FOR THE SAMPLE WITH 15N-LABELED PROTEIN. SIGNALS DUE TO DNA WERE OBTAINED BY NOESY, TOCSY, AND DQF-COSY FOR UNLABELED SAMPLE AND 13C,15N-FILTERED NOESY FOR SAMPLE WITH 13C, 15N-LABELED PROTEIN. INTERMOLECULAR NOES WERE IDENTIFIED USING NOESY SPECTRA INCLUDING THOSE WITH AND WITHOUT 13C- OR 15N-DECOUPLING FOR SAMPLE WITH 13C,15N-LABELED PROTEIN. |
-Sample preparation
Details | Contents: POTASIUM PHOSPHATE |
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Sample conditions | Ionic strength: 90 mM / pH: 6.0 / Pressure: 1 ATMOSPHERE / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: SIMULATED ANNEALING PROTOCOL IN X-PLOR 3.1 WAS CARRIED OUT TO OBTAIN 25 STRUCTURES. MINIMIZED MEAN STRUCTURE OF THEM WAS FURTHER REVISED BY A 300 PS RESTRAINED MOLECULAR DYNAMICAL CALCULATION ...Method: SIMULATED ANNEALING PROTOCOL IN X-PLOR 3.1 WAS CARRIED OUT TO OBTAIN 25 STRUCTURES. MINIMIZED MEAN STRUCTURE OF THEM WAS FURTHER REVISED BY A 300 PS RESTRAINED MOLECULAR DYNAMICAL CALCULATION IN THE PRESENCE OF APPROXIMATELY 5000 TIP3P WATER MOLSCULES, USING CORNELL FORCE FIELD IN AMBER 4.1. THE MEAN CO-ORDINATE OF 200 STRUCTURES OBTAINED AFTER THE EQUILIBRIUM (100 PS) WAS ENERGY-MINIMIZED. Software ordinal: 1 Details: SEE REMARK 210 OTHER PROGRAMS USED: AMBER 4.1 AUTHORS: PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM III, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN | ||||||||||||||||
NMR ensemble | Conformers calculated total number: 1 / Conformers submitted total number: 1 |