6E9C | pdb_00006e9c

Selenomethionine Derivative Structure of A Bacterial Homolog to Human Lysosomal Transporter, Spinster

• PDB DOI: https://doi.org/10.2210/pdb6E9C/pdb

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


• Deposited: 2018-07-31 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.04 kDa 
• Atom Count: 3,628 
• Modeled Residue Count: 479 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.59	α = 90
b = 87.33	β = 90
c = 122.26	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Zhou, F., Yao, D., Rao, B., Zhang, L., Cao, Y.

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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  

• 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