Maintance Thur 2026 Nov 12

The SBDB will be undergoing infrastructure maintance Thur 2026 Nov 12 between 10AM and 6PM ET. Dataset registrations, dataset depositions, and dataset downloads from the primary location will be unavailable; API access will also be impacted.

X-Ray Diffraction data from human Dcytb in complex with Zn and ascorbate, source of 5ZLG structure

dataset logo thumbnail
Visualize in 3D >>

Data DOI: 10.15785/SBGRID/574 | ID: 574

Publication DOI: 10.1038/s42003-018-0121-8

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

Shiro Laboratory, University of Hyogo

Release Date: 17 Aug 2018

Data Access Instructions

1. If this dataset is locally available, it should be accessable at /programs/datagrid/574

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/574 .' (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/574 .' (Uppsala University, Sweden)

'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/574 .' (Institut Pasteur de Montevideo, Uruguay)

'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/574 .' (Shanghai Institutes for Biological Sciences, China)

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

'cd 574 ; shasum -c files.sha'

Storage requirements: 262G

Biological Sample:

human Dcytb in complex with Zn and ascorbate

Dataset Type:

X-Ray Diffraction

Subject Composition:

Ligand, Protein

Collection Facility:

SPring-8 beamline BL32XU

Data Creation Date:

1 Dec 2016

Related Datasets:

None


Cite this Dataset

Yamashita, K; Ganasen, M; Mauk, GA; Sawai, H; Sugimoto, H; Togashi, H; Shiro, Y. 2018. "X-Ray Diffraction data for: human Dcytb in complex with Zn and ascorbate. PDB Code 5ZLG", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/574.

Download Citation

Dataset Description

Small-wedge (5 degrees/crystal) data collected using 5x5 um beam

Project Members

Name Additional Roles Affiliation While Working on the Project
Keitaro YamashitaDepositorRIKEN SPring-8 Center
Menega GanasenUniversity of Hyogo
Grant A MaukUniversity of British Columbia
Hitomi SawaiUniversity of Hyogo
Hiroshi SugimotoData CollectorRIKEN SPring-8 Center
Hiromi TogashiRIKEN SPring-8 Center
Yoshitsugu ShiroPIUniversity of Hyogo

Reprocessing Instructions

600 datasets were merged at 2.8 Å resolution in the published result using KAMO (XDS/XSCALE used for integration/merging); see https://github.com/keitaroyam/yamtbx/wiki/Processing-Dcytb-data-(5ZLE-&-5ZLG)

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//574/ 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//574/ 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//574/ 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.