6JJ9 | pdb_00006jj9

Crystal structure of OsHXK6-Glc-ATP-Mg2+ complex

• PDB DOI: https://doi.org/10.2210/pdb6JJ9/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Oryza sativa Japonica Group
• Expression System: Oryza sativa
• Mutation(s): No 


• Deposited: 2019-02-25 Released: 2019-07-03 
• Deposition Author(s): He, C., Wei, P., Chen, J., Wang, H., Wan, Y., Zhou, J., Zhu, Y., Huang, W., Yin, L.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of OsHXK6-Glc-ATP-Mg2+ complex

He, C., Wei, P., Chen, J., Wang, H., Wan, Y., Zhou, J., Zhu, Y., Huang, W., Yin, L.

To be published.

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: native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 155.49 kDa 
• Atom Count: 10,902 
• Modeled Residue Count: 1,395 
• Deposited Residue Count: 1,395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase-6	A [auth C], B [auth A], C [auth E]	465	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: HXK6, HXK2, Os01g0742500, LOC_Os01g53930, P0439E07.19 EC: 2.7.1.1
UniProt
Find proteins for Q8LQ68 (Oryza sativa subsp. japonica) Explore Q8LQ68  Go to UniProtKB:  Q8LQ68

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth C], H [auth A], L [auth E]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BGC	G [auth C], K [auth A], O [auth E]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	E [auth C], I [auth A], M [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	F [auth C], J [auth A], N [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.12	α = 90
b = 131.12	β = 90
c = 186.192	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): He, C., Wei, P., Chen, J., Wang, H., Wan, Y., Zhou, J., Zhu, Y., Huang, W., Yin, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	--

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary