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- SASDCF6: HIT family hydrolase protein from Vibrio fischeri. Northeast Stru... -

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Basic information

Entry
Database: SASBDB / ID: SASDCF6
SampleHIT family hydrolase protein from Vibrio fischeri. Northeast Structural Genomics Consortium target id VfR176
  • HIT family hydrolase (protein), Vibrio fischeri (strain ATCC 700601 / ES114)
Function / homologyHistidine triad hydrolase, Hint-type / HIT domain / HIT domain profile. / HIT-like domain / HIT-like superfamily / hydrolase activity / HIT family hydrolase
Function and homology information
Biological speciesVibrio fischeri (strain ATCC 700601 / ES114) (bacteria)
CitationJournal: Biopolymers / Year: 2011
Title: Small angle X-ray scattering as a complementary tool for high-throughput structural studies.
Authors: Thomas D Grant / Joseph R Luft / Jennifer R Wolfley / Hiro Tsuruta / Anne Martel / Gaetano T Montelione / Edward H Snell /
Abstract: Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained ...Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. Although powerful techniques, they leave many soluble, purified structurally uncharacterized protein samples. Small angle X-ray scattering (SAXS) is a solution technique that provides data on the size and multiple conformations of a sample, and can be used to reconstruct a low-resolution molecular envelope of a macromolecule. In this study, SAXS has been used in a high-throughput manner on a subset of 28 proteins, where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low-resolution technique that can provide additional structural information in a high-throughput and complementary manner to improve the functional interpretation of high-resolution structures.

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Structure visualization

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Models

Model #1428
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 3.908529
Search similar-shape structures of this assembly by Omokage search (details)
Model #1430
Type: dummy / Radius of dummy atoms: 2.00 A / Chi-square value: 2.396304
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: HIT family hydrolase protein from Vibrio fischeri. Northeast Structural Genomics Consortium target id VfR176
Specimen concentration: 2.08-6.26
BufferName: 5 mM DTT 100 mM NaCl 10 mM Tris-HCl 0.02 % NaN3 / pH: 7.5
Entity #750Type: protein / Description: HIT family hydrolase / Formula weight: 16.995 / Num. of mol.: 2 / Source: Vibrio fischeri (strain ATCC 700601 / ES114) / References: UniProt: Q5E3V1
Sequence:
MAFQLHPRLQ QDCIVLGNLP LCKVLLIKED IGPWLILVPR IEELKEIHHM TDEQQIQFIK ESSAVAQLLE DNFSPDKINI GALGNLVPQL HIHHIARFTT DVAWPGPVWG NTTGVIRAQS SQTQLVDLLR DKLSNISGFK RLEHHHHHH

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Experimental information

BeamInstrument name: Stanford Synchrotron Radiation Lightsource (SSRL) BL4-2
City: Stanford, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.13 Å / Dist. spec. to detc.: 1.5 mm
DetectorName: Rayonix MX225-HE
Scan
Title: HIT family hydrolase protein from Vibrio fischeri. Northeast Structural Genomics Consortium target id VfR176
Measurement date: Feb 12, 2010 / Storage temperature: -80 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 20 / Unit: 1/A /
MinMax
Q0.0169 0.3496
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 345 /
MinMax
Q0.02897 0.3496
P(R) point13 357
R0 71.45
Result
D max: 7.15 / Type of curve: single_conc /
ExperimentalPorod
MW34.79 kDa34.79 kDa
Volume-57.75 nm3

P(R)Guinier
Forward scattering, I01059 1061.36
Radius of gyration, Rg2.12 nm2.12 nm

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