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- PDB-1d8b: NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RE... -
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Basic information
Entry | Database: PDB / ID: 1d8b | ||||||
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Title | NMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE | ||||||
![]() | SGS1 RECQ HELICASE | ||||||
![]() | DNA BINDING PROTEIN / FIVE HELICES / THREE-HELICAL BUNDLE FLANKED BY TWO HELICES | ||||||
Function / homology | ![]() negative regulation of meiotic joint molecule formation / gene conversion at mating-type locus => GO:0007534 / regulation of reciprocal meiotic recombination / : / meiotic DNA double-strand break processing / telomeric 3' overhang formation / RecQ family helicase-topoisomerase III complex / meiotic chromosome segregation / four-way junction helicase activity / DNA double-strand break processing ...negative regulation of meiotic joint molecule formation / gene conversion at mating-type locus => GO:0007534 / regulation of reciprocal meiotic recombination / : / meiotic DNA double-strand break processing / telomeric 3' overhang formation / RecQ family helicase-topoisomerase III complex / meiotic chromosome segregation / four-way junction helicase activity / DNA double-strand break processing / telomere maintenance via recombination / mitotic G2/M transition checkpoint / mitotic intra-S DNA damage checkpoint signaling / DNA duplex unwinding / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / mitotic sister chromatid segregation / DNA topological change / chromosome organization / DNA helicase activity / telomere maintenance / double-strand break repair via homologous recombination / chromosome / DNA recombination / DNA helicase / nucleic acid binding / DNA repair / nucleolus / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / ARIA (AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENTS) AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS | ||||||
![]() | Liu, Z. / Macias, M.J. / Bottomley, M.J. / Stier, G. / Linge, J.P. / Nilges, M. / Bork, P. / Sattler, M. | ||||||
![]() | ![]() Title: The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins. Authors: Liu, Z. / Macias, M.J. / Bottomley, M.J. / Stier, G. / Linge, J.P. / Nilges, M. / Bork, P. / Sattler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 431.1 KB | Display | ![]() |
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PDB format | ![]() | 367.4 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 348 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 9385.962 Da / Num. of mol.: 1 / Fragment: HRDC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 20 mM SODIUM PHOSPHATE / pH: 6.5 / Pressure: 1 bar / Temperature: 295 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: ARIA (AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENTS) AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS Software ordinal: 1 Details: STARTING WITH AN ALMOST COMPLETE LIST OF CHEMICAL SHIFTS, THE PROGRAM ARIA ( AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENT) CALIBRATES NOES, MERGES THE OBTAINED AMBIGUOUS DISTANCE RESTRAINTS ...Details: STARTING WITH AN ALMOST COMPLETE LIST OF CHEMICAL SHIFTS, THE PROGRAM ARIA ( AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENT) CALIBRATES NOES, MERGES THE OBTAINED AMBIGUOUS DISTANCE RESTRAINTS FROM DIFFERENT NOE SPECTRA AND ASSIGNS THE NOE PEAKS IN AN ITERATIVE MANNER. FROM A TOTAL OF 1890 NOES ABOUT 85% WERE MANUALLY ASSIGNED, THE REMAINDER WAS ASSIGNED BY ARIA. FLOATING POINT CHIRALITY ASSIGNMENT WAS USED DURING THE STRUCTURE CALCULATION IN ORDER TO OBTAIN STEREOSPECIFIC ASSIGNMENTS FOR METHYL AND METHYLENE GROUPS. THEREFORE, SOME METHYL AND METHYLENE CARBON/PROTON ATOM NAMES IN THE RESTRAINT FILES MIGHT BE INCONSISTENT COMPARED TO THOSE IN THE COORIDINATE FILES. THE DEPOSITED STRUCTURES HAVE BEEN WATER-REFINED AS DESCRIBED IN THE PUBLICATION. PSI REFINEMENT: THE STRUCTURES HAVE BEEN DIRECTLY REFINED AGAINST CROSS- CORRELATED RELAXATION RATES (C-ALPHA-H-ALPHA DIPOLE, CO CSA) AND THE THREE- BOND H/D ISOTOPE EFFECT ON THE C-ALPHA CHEMICAL SHIFT. "REFINEMENT OF THE PROTEIN BACKBONE ANGLE PSI IN NMR STRUCTURE CALCULATIONS." SPRANGERS, BOTTOMLEY, LINGE, SCHULTZ, NILGES, SATTLER. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND ENERGY Conformers calculated total number: 100 / Conformers submitted total number: 15 |