6JJ7 | pdb_00006jj7

Crystal structure of OsHXK6-Glc complex

PDB DOI: https://doi.org/10.2210/pdb6JJ7/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.248 (Depositor), 0.253 (DCC)
R-Value Work:
0.200 (Depositor), 0.210 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of OsHXK6-Glc complex

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

To be published.

Macromolecule Content

Total Structure Weight: 153.86 kDa
Atom Count: 10,803
Modeled Residue Count: 1,395
Deposited Residue Count: 1,395
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rice hexokinase 6	A, B [auth C], 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8LQ68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth C] SDF format, chain F [auth E] MOL2 format, chain D [auth A] MOL2 format, chain E [auth C] MOL2 format, chain F [auth E] mmCIF format, chain D [auth A] mmCIF format, chain E [auth C] mmCIF format, chain F [auth E]	D [auth A], E [auth C], F [auth E]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth C] Focus chain F [auth E] Interactions & Density Focus chain D [auth A] Focus chain E [auth C] Focus chain F [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.248 (Depositor), 0.253 (DCC)
R-Value Work: 0.200 (Depositor), 0.210 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.569	α = 90
b = 131.569	β = 90
c = 188.782	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

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

Revision History (Full details and data files)

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