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- SASDCK2: Glucose Isomerase - Streptomyces rubiginosus (Xylose isomerase, G... -

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Basic information

Entry
Database: SASBDB / ID: SASDCK2
SampleGlucose Isomerase - Streptomyces rubiginosus
  • Xylose isomerase (protein), Glucose Isomerase, Streptomyces rubiginosus
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
CitationJournal: 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
  • Jill Trewhella (School of Molecular Bioscience, University of Sydney., Sydney, New South Wales 2006, Australia)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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Sample

SampleName: Glucose Isomerase - Streptomyces rubiginosus / Specimen concentration: 0.06-0.34
BufferName: 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 #612Name: Glucose 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

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Experimental information

BeamInstrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotron / Wavelength: 0.10332 Å / Dist. spec. to detc.: 2.683 mm
DetectorName: 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 /
MinMax
Q0.0066 0.3104
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 304 /
MinMax
Q0.00662753 0.242734
P(R) point1 304
R0 92.15
Result
Type of curve: other
ExperimentalStandardPorod
MW172.234 kDa183.254 kDa152.667 kDa
Volume--229 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.03739 3.9E-5 0.037 4.4E-5
Radius of gyration, Rg3.265 nm0.004 3.287 nm0.013

MinMax
D-9.22
Guinier point1 43

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