[English] 日本語
Yorodumi
- PDB-6jj9: Crystal structure of OsHXK6-Glc-ATP-Mg2+ complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jj9
TitleCrystal structure of OsHXK6-Glc-ATP-Mg2+ complex
ComponentsHexokinase-6
KeywordsSTRUCTURAL PROTEIN / Hexokinase ATP phosphorylation
Function / homology
Function and homology information


hexose metabolic process / chloroplast outer membrane / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / glucose 6-phosphate metabolic process / glucose binding / cellular glucose homeostasis / response to glucose ...hexose metabolic process / chloroplast outer membrane / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / glucose 6-phosphate metabolic process / glucose binding / cellular glucose homeostasis / response to glucose / glycolytic process / mitochondrion / integral component of membrane / ATP binding / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, binding site / Hexokinase / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, binding site / Hexokinase / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / beta-D-glucopyranose / PHOSPHATE ION / Hexokinase-6
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHe, C. / Wei, P. / Chen, J. / Wang, H. / Wan, Y. / Zhou, J. / Zhu, Y. / Huang, W. / Yin, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To Be Published
Title: Crystal structure of OsHXK6-Glc-ATP-Mg2+ complex
Authors: He, C. / Wei, P. / Chen, J. / Wang, H. / Wan, Y. / Zhou, J. / Zhu, Y. / Huang, W. / Yin, L.
History
DepositionFeb 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Hexokinase-6
A: Hexokinase-6
E: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,49515
Polymers153,3153
Non-polymers2,18012
Water0
1
C: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8325
Polymers51,1051
Non-polymers7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-7 kcal/mol
Surface area19340 Å2
MethodPISA
2
A: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8325
Polymers51,1051
Non-polymers7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19440 Å2
MethodPISA
3
E: Hexokinase-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8325
Polymers51,1051
Non-polymers7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-7 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.120, 131.120, 186.192
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Hexokinase-6 / / Hexokinase-2


Mass: 51105.004 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: HXK6, HXK2, Os01g0742500, LOC_Os01g53930, P0439E07.19 / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: Q8LQ68, hexokinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 2 mM D-glucose, 3 mM magnesium chloride, 2 mM ATP, 0.1 M MES 6.5, 0.05 M cesium chloride, 30% v/v JeffamineM-600.

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→43.07 Å / Num. obs: 37637 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.02402 / Net I/σ(I): 19.94
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 0.07885 / Mean I/σ(I) obs: 8.15 / Num. unique obs: 3702

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JJ7
Resolution: 3→43.07 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.02
RfactorNum. reflection% reflection
Rfree0.2422 1989 5.28 %
Rwork0.2065 --
obs0.2084 37637 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10863 0 39 0 10902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311091
X-RAY DIFFRACTIONf_angle_d0.7115012
X-RAY DIFFRACTIONf_dihedral_angle_d21.6436627
X-RAY DIFFRACTIONf_chiral_restr0.0441698
X-RAY DIFFRACTIONf_plane_restr0.0031938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.07530.30411390.24762509X-RAY DIFFRACTION100
3.0753-3.15840.31671410.25332533X-RAY DIFFRACTION100
3.1584-3.25130.3021370.24012507X-RAY DIFFRACTION100
3.2513-3.35620.26151440.23452515X-RAY DIFFRACTION100
3.3562-3.47620.27181420.22342488X-RAY DIFFRACTION100
3.4762-3.61530.25271410.21772535X-RAY DIFFRACTION100
3.6153-3.77980.25361380.21692528X-RAY DIFFRACTION100
3.7798-3.9790.24921430.20862533X-RAY DIFFRACTION100
3.979-4.22810.24391410.20272546X-RAY DIFFRACTION100
4.2281-4.55440.21061440.18082535X-RAY DIFFRACTION100
4.5544-5.01230.21331420.18132544X-RAY DIFFRACTION100
5.0123-5.73660.25211440.20182569X-RAY DIFFRACTION100
5.7366-7.22360.22811410.21792600X-RAY DIFFRACTION100
7.2236-48.47950.21041520.18392708X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more