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

Basic information

• Entry: Database: SASBDB / ID: SASDCK2

Sample

Glucose Isomerase - Streptomyces rubiginosus

• Xylose isomerase (protein), Glucose IsomeraseXylose isomerase, Streptomyces rubiginosus

Function / homology

Function:

xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm

Domain/homology:

Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily

Component:

Xylose isomerase

• 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 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 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)

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 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 /

	Min	Max
Q	0.0066	0.3104

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 304 /

	Min	Max
Q	0.00662753	0.242734
P(R) point	1	304
R	0	92.15

Result

Type of curve: other

	Experimental	Standard	Porod
MW	172.234 kDa	183.254 kDa	152.667 kDa
Volume	-	-	229 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.03739	3.9E-5	0.037	4.4E-5
Radius of gyration, Rg	3.265 nm	0.004	3.287 nm	0.013

	Min	Max
D	-	9.22
Guinier point	1	43