SASDAB6: Xylose Isomerase (GI Glucose isomerase)

Basic information

• Entry: Database: SASBDB / ID: SASDAB6

Sample

Xylose Isomerase

• Xylose Isomerase (protein), GI Glucose isomerase, Streptomyces rubiginosus

• Biological species: Streptomyces rubiginosus (bacteria)
• Citation: Journal: Nat Methods / Year: 2015; Title: Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.; Authors: Daniel Franke / Cy M Jeffries / Dmitri I Svergun / ; Abstract: Assessing similarity between data sets with the reduced χ(2) test requires the estimation of experimental errors, which, if incorrect, may render statistical comparisons invalid. We report a goodness-of-fit test, Correlation Map (CorMap), for assessing differences between one-dimensional spectra independently of explicit error estimates, using only data point correlations. Using small-angle X-ray scattering data, we demonstrate that CorMap maintains the power of the reduced χ(2) test; moreover, CorMap is also applicable to other physical experiments.

Contact author

• Dmitri Svergun
• Cy M Jeffries
• Daniel Franke

Models

• Model #173: ; Type: dummy / Radius of dummy atoms: 1.90 A / Symmetry: P4 / Chi-square value: 1.354896; Search similar-shape structures of this assembly by Omokage search (details)
• Model #174: ; Type: atomic / Software: (3.0) / Comment: Based on PDB 4E3V / Chi-square value: 1.411344; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Xylose Isomerase / Ext coefficient: 1.075 / Purity method: Crystalline, Hampton Research / Specimen concentration: 5.76 mg/ml / Concentration method: A280 nm
• Buffer: Name: 20 mM HEPES 200 mM Na2SO4 50 mM K2SO4 500 % v/v D2O 1 mM MgCl2; Concentration: 20.00 mM / pH: 6.6 / Comment: pD = 7.0; Composition: Na2SO4 200.000 mM, K2SO4 50.000 mM, D2O 50.000 % v/v, MgCl2 1.000 mM

Entity #121

Name: GI Glucose isomerase / Type: protein / Description: Xylose Isomerase / Formula weight: 43.2 / Num. of mol.: 4 / Source: Streptomyces rubiginosus
Sequence:

MNYQPTPEDR FTFGLWTVGW QGRDPFGDAT RRALDPVESV RRLAELGAHG VTFHDDDLIP FGSSDSEREE HVKRFRQALD DTGMKVPMAT TNLFTHPVFK DGGFTANDRD VRRYALRKTI RNIDLAVELG AETYVAWGGR EGAESGGAKD VRDALDRMKE AFDLLGEYVT SQGYDIRFAI EPKPNEPRGD ILLPTVGHAL AFIERLERPE LYGVNPEVGH EQMAGLNFPH GIAQALWAGK LFHIDLNGQN GIKYDQDLRF GAGDLRAAFW LVDLLESAGY SGPRHFDFKP PRTEDFDGVW ASAAGCMRNY LILKERAAAF RADPEVQEAL RASRLDELAR PTAADGLQAL LDDRSAFEEF DVDAAAARGM AFERLDQLAM DHLLGARGMN YQPTPEDRFT FGLWTVGWQG RDPFGDATRR ALDPVESVRR LAELGAHGVT FHDDDLIPFG SSDSEREEHV KRFRQALDDT GMKVPMATTN LFTHPVFKDG GFTANDRDVR RYALRKTIRN IDLAVELGAE TYVAWGGREG AESGGAKDVR DALDRMKEAF DLLGEYVTSQ GYDIRFAIEP KPNEPRGDIL LPTVGHALAF IERLERPELY GVNPEVGHEQ MAGLNFPHGI AQALWAGKLF HIDLNGQNGI KYDQDLRFGA GDLRAAFWLV DLLESAGYSG PRHFDFKPPR TEDFDGVWAS AAGCMRNYLI LKERAAAFRA DPEVQEALRA SRLDELARPT AADGLQALLD DRSAFEEFDV DAAAARGMAF ERLDQLAMDH LLGARGMNYQ PTPEDRFTFG LWTVGWQGRD PFGDATRRAL DPVESVRRLA ELGAHGVTFH DDDLIPFGSS DSEREEHVKR FRQALDDTGM KVPMATTNLF THPVFKDGGF TANDRDVRRY ALRKTIRNID LAVELGAETY VAWGGREGAE SGGAKDVRDA LDRMKEAFDL LGEYVTSQGY DIRFAIEPKP NEPRGDILLP TVGHALAFIE RLERPELYGV NPEVGHEQMA GLNFPHGIAQ ALWAGKLFHI DLNGQNGIKY DQDLRFGAGD LRAAFWLVDL LESAGYSGPR HFDFKPPRTE DFDGVWASAA GCMRNYLILK ERAAAFRADP EVQEALRASR LDELARPTAA DGLQALLDDR SAFEEFDVDA AAARGMAFER LDQLAMDHLL GARGMNYQPT PEDRFTFGLW TVGWQGRDPF GDATRRALDP VESVRRLAEL GAHGVTFHDD DLIPFGSSDS EREEHVKRFR QALDDTGMKV PMATTNLFTH PVFKDGGFTA NDRDVRRYAL RKTIRNIDLA VELGAETYVA WGGREGAESG GAKDVRDALD RMKEAFDLLG EYVTSQGYDI RFAIEPKPNE PRGDILLPTV GHALAFIERL ERPELYGVNP EVGHEQMAGL NFPHGIAQAL WAGKLFHIDL NGQNGIKYDQ DLRFGAGDLR AAFWLVDLLE SAGYSGPRHF DFKPPRTEDF DGVWASAAGC MRNYLILKER AAAFRADPEV QEALRASRLD ELARPTAADG LQALLDDRSA FEEFDVDAAA ARGMAFERLD QLAMDHLLGA RG

Experimental information

• Beam: Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Xylose Isomerase / Measurement date: Dec 10, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0907	3.5006

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1048 /

	Min	Max
Q	0.0906896	2.84546
P(R) point	1	1048
R	0	9.12

Result

Type of curve: single_conc / Standard: BSA
Comments: The data displayed at the top of the entry, and the subsequent ab inito and atomic model fit, are data derived from averaging 20 individual frames. The individual 20 data frames used for the averaging are also displayed, with the respective atomic-model fits (CRYSOL; PDB 4E3V).

	Experimental	Standard	Porod
MW	149 kDa	149 kDa	137.3 kDa
Volume	-	-	233.5 nm3

	P(R)	Guinier
Forward scattering, I0	3770	3733.8
Radius of gyration, Rg	3.24 nm	3.21 nm

	Min	Max
D	-	9.1
Guinier point	1	121