[English] 日本語
Yorodumi- SASDCK2: Glucose Isomerase - Streptomyces rubiginosus (Xylose isomerase, G... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDCK2 |
---|---|
Sample | Glucose Isomerase - Streptomyces rubiginosus
|
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function |
Biological species | Streptomyces rubiginosus (bacteria) |
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Authors: Jill Trewhella / Anthony P Duff / Dominique Durand / Frank Gabel / J Mitchell Guss / Wayne A Hendrickson / Greg L Hura / David A Jacques / Nigel M Kirby / Ann H Kwan / Javier Pérez / Lois ...Authors: Jill Trewhella / Anthony P Duff / Dominique Durand / Frank Gabel / J Mitchell Guss / Wayne A Hendrickson / Greg L Hura / David A Jacques / Nigel M Kirby / Ann H Kwan / Javier Pérez / Lois Pollack / Timothy M Ryan / Andrej Sali / Dina Schneidman-Duhovny / Torsten Schwede / Dmitri I Svergun / Masaaki Sugiyama / John A Tainer / Patrice Vachette / John Westbrook / Andrew E Whitten / Abstract: In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle ...In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field. |
Contact author |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Data source
SASBDB page | SASDCK2 |
---|
-Related structure data
Related structure data | C: citing same article (ref.) |
---|---|
Similar structure data |
-External links
Related items in Molecule of the Month |
---|
-Models
Model #1173 | Type: dummy / Software: (on-line) / Radius of dummy atoms: 2.40 A / Symmetry: P1 / Comment: job submitted ATSAS on-line April 9, 2017 / Chi-square value: 0.951 / P-value: 0.035000 Search similar-shape structures of this assembly by Omokage search (details) |
---|---|
Model #1174 | Type: atomic / Software: (on-line) / Radius of dummy atoms: 1.90 A Comment: GI tetramer generated from PDB:1OAD using symmetry transforms in pymol Chi-square value: 1.01580033274 / P-value: 0.045511 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: Glucose Isomerase - Streptomyces rubiginosus / Specimen concentration: 0.06-0.34 |
---|---|
Buffer | Name: 25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3 pH: 7.5 Comment: 2 mM TCEP and 0.1% (.01538 M) NaN3 used for radiation protection |
Entity #612 | Name: Glucose IsomeraseXylose isomerase / Type: protein / Description: Xylose isomerase / Formula weight: 43.097 / Num. of mol.: 4 / Source: Streptomyces rubiginosus / References: UniProt: P24300 Sequence: NYQPTPEDRF TFGLWTVGWE GRDPFGDATR RALDPVESVR RLAELGAHGV TFHDDDLIPF GSSDSEREEH VKRFRQALDD TGMKVPMATT NLFTHPVFKD GGFTANDRDV RRYALRKTIR NIDLAVELGA ETYVAWGGRE GAESGGAKDV RDALDRMKEA FDLLGEYVTS ...Sequence: NYQPTPEDRF TFGLWTVGWE GRDPFGDATR RALDPVESVR RLAELGAHGV TFHDDDLIPF GSSDSEREEH VKRFRQALDD TGMKVPMATT NLFTHPVFKD GGFTANDRDV RRYALRKTIR NIDLAVELGA ETYVAWGGRE GAESGGAKDV RDALDRMKEA FDLLGEYVTS QGYDIRFAIE PKPNEPRGDI LLPTVGHALA FIERLERPEL YGVNPEVGHE QMAGLNFPHG IAQALWAGKL FHIDLNGQNG IKYDQDLRFG AGDLRAAFWL VDLLESAGYS GPRHFDFKPP RTEDFDGVWA SAAGCMRNYL ILKERAAAFR ADPEVQEALR ASRLDELARP TAADGLQALL DDRSAFEEFD VDAAAARGMA FERLDQLAMD HLLGARG |
-Experimental information
Beam | Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.10332 Å / Dist. spec. to detc.: 2.683 mm | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm | ||||||||||||||||||||||||||||||||||||
Scan | Title: Glucose Isomerase - Streptomyces rubiginosus / Measurement date: Mar 9, 2017 / Cell temperature: 22 °C / Exposure time: 1 sec. / Number of frames: 24 / Unit: 1/A /
| ||||||||||||||||||||||||||||||||||||
Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 304 /
| ||||||||||||||||||||||||||||||||||||
Result | Type of curve: other
|