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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
TitleNMR STRUCTURE OF THE HRDC DOMAIN FROM SACCHAROMYCES CEREVISIAE RECQ HELICASE
ComponentsSGS1 RECQ HELICASE
KeywordsDNA BINDING PROTEIN / FIVE HELICES / THREE-HELICAL BUNDLE FLANKED BY TWO HELICES
Function / homology
Function and homology information


negative regulation of meiotic joint molecule formation / regulation of reciprocal meiotic recombination / meiotic DNA double-strand break processing / : / gene conversion at mating-type locus / telomeric 3' overhang formation / RecQ family helicase-topoisomerase III complex / : / : / meiotic chromosome segregation ...negative regulation of meiotic joint molecule formation / regulation of reciprocal meiotic recombination / meiotic DNA double-strand break processing / : / gene conversion at mating-type locus / telomeric 3' overhang formation / RecQ family helicase-topoisomerase III complex / : / : / meiotic chromosome segregation / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / cohesin loader activity / ATP-dependent H3-H4 histone complex chaperone activity / DNA double-strand break processing / telomere maintenance via recombination / DNA clamp loader activity / mitotic G2/M transition checkpoint / mitotic intra-S DNA damage checkpoint signaling / 3'-5' DNA helicase activity / DNA 3'-5' helicase / DNA topological change / mitotic sister chromatid segregation / chromosome organization / DNA helicase activity / telomere maintenance / isomerase activity / double-strand break repair via homologous recombination / chromosome / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / nucleolus / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
ATP-dependent helicase Sgs1 / Sgs1 RecQ helicase / HRDC domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain ...ATP-dependent helicase Sgs1 / Sgs1 RecQ helicase / HRDC domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / HRDC domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent helicase SGS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / ARIA (AMBIGUOUS RESTRAINTS IN ITERATIVE ASSIGNMENTS) AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS
AuthorsLiu, Z. / Macias, M.J. / Bottomley, M.J. / Stier, G. / Linge, J.P. / Nilges, M. / Bork, P. / Sattler, M.
CitationJournal: Structure Fold.Des. / Year: 1999
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
DepositionOct 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2000Provider: 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 ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SGS1 RECQ HELICASE


Theoretical massNumber of molelcules
Total (without water)9,3861
Polymers9,3861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein SGS1 RECQ HELICASE


Mass: 9385.962 Da / Num. of mol.: 1 / Fragment: HRDC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P35187

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1223D 15N-SEPARATED NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
113C-15N-LABELED SAMPLE20 mM sodium phosphate buffer
215N-LABELED SAMPLE20 mM sodium phosphate buffer
Sample conditionsIonic strength: 20 mM SODIUM PHOSPHATE / pH: 6.5 / Pressure: 1 bar / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7DELAGLIOprocessing
XEASY1.3.13BARTELS, XIA, BILLETER, GUENTERT, WUETHRICHdata analysis
ARIA0.9LINGE, O'DONOGHUE, NILGESstructure solution
ARIA0.9LINGE, O'DONOGHUE, NILGESiterative matrix relaxation
CNS0.9BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENstructure solution
CNS0.9BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 15

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