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X-Ray Diffraction data from Triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate, source of 5Y79 structure

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Data DOI: 10.15785/SBGRID/512 | ID: 512

Publication DOI: 10.1038/s41477-017-0022-8

5Y79 Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB

Nureki Laboratory, The University of Tokyo

Release Date: 27 Oct 2017

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/512

2. To download this dataset, please run the following command from your Terminal on a Linux or OS X workstation:

'rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/512 .' (Harvard Medical School, USA)

Depending on your location, faster access may be available from a Tier 1 site closer to your location

'rsync -av rsync://sbgrid.icm.uu.se/10.15785/SBGRID/512 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/512 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/512 .' (Shanghai Institutes for Biological Sciences, China)

3. After the transfer is completed, please issue the following command to verify data integrity:

'cd 512 ; shasum -c files.sha'

Storage requirements: 107G

Biological Sample:

Triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate

Dataset Type:

X-Ray Diffraction

Subject Composition:

Ligand, Protein

Collection Facility:

SPring-8 beamline BL32XU

Data Creation Date:

21 Sep 2016

Related Datasets:

None


Cite this Dataset

Yamashita, K; Hirata, K; Lee, Y; Nureki, O. 2017. "X-Ray Diffraction data for: Triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate. PDB Code 5Y79", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/512.

Download Citation

Dataset Description

Triose-phosphate/phosphate translocator in complex with 3-phosphoglycerate

Project Members

Name Additional Roles Affiliation While Working on the Project
Keitaro YamashitaDepositorRIKEN SPring-8 Center
Kunio HirataRIKEN SPring-8 Center
Yongchan LeeData CollectorDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo
Osamu NurekiPIThe University of Tokyo

Reprocessing Instructions

199 datasets were merged at 2.2 Å resolution in the published result using KAMO (XDS/XSCALE used for integration/merging); see https://github.com/keitaroyam/yamtbx/wiki/Processing-TPT-data-(5Y78-&-5Y79)

Reprocessing Data

About Reprocessing

xia2 -2d

xia2 -3d

xia2 -3dii

xia2 -dials
/programs/x86_64-linux/dials/3.12.0/bin.capsules//xia2 pipeline=3d /programs/datagrid//512/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/3.12.0/bin.capsules//xia2 pipeline=3dii /programs/datagrid//512/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.

/programs/x86_64-linux/dials/3.12.0/bin.capsules//xia2 pipeline=dials /programs/datagrid//512/ verbose=True multiprocessing.nproc=1 atom=X

Version:

version unreported

Reprocessing failed.


License and Terms of use

License: CC0

Terms: Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation, as generated by the SBGrid Data Bank.