6E8J | pdb_00006e8j

Crystal Structure of A Bacterial Homolog to Human Lysosomal Transporter, Spinster, in Inward-facing And Occupied Conformation

PDB DOI: https://doi.org/10.2210/pdb6E8J/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Hyphomonas neptunium ATCC 15444
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2018-07-30 Released: 2019-08-14
Deposition Author(s): Zhou, F., Yao, D., Rao, B., Zhang, L., Cao, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC), National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.298 (Depositor), 0.304 (DCC)
R-Value Work:
0.257 (Depositor), 0.263 (DCC)
R-Value Observed:
0.261 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a bacterial homolog to human lysosomal transporter, spinster

Zhou, F., Yao, D., Rao, B., Zhang, L., Nie, W., Zou, Y., Zhao, J.,, Cao, Y.

(2019) Sci Bull (Beijing) 64: 1310-1317

DOI: https://doi.org/10.1016/j.scib.2019.08.010

Macromolecule Content

Total Structure Weight: 54.29 kDa
Atom Count: 3,519
Modeled Residue Count: 465
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major facilitator family transporter	A	508	Hyphomonas neptunium ATCC 15444	Mutation(s): 0 Gene Names: HNE_0949 Membrane Entity: Yes
UniProt
Find proteins for Q0C3L7 (Hyphomonas neptunium (strain ATCC 15444)) Explore Q0C3L7 Go to UniProtKB: Q0C3L7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0C3L7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.298 (Depositor), 0.304 (DCC)
R-Value Work: 0.257 (Depositor), 0.263 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.709	α = 90
b = 89.419	β = 90
c = 122.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U1632132
National Natural Science Foundation of China (NSFC)	China	31670849
National Basic Research Program of China (973 Program)	China	2017YFC1001303

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2019-09-25
Changes: Data collection, Database references
Version 1.2: 2020-01-08
Changes: Author supporting evidence, Database references
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.