[English] 日本語
Yorodumi
- PDB-5htx: Putative sugar kinases from Arabidopsis thaliana in complex with ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5htx
TitlePutative sugar kinases from Arabidopsis thaliana in complex with ADP
ComponentsPutative xylulose kinase
KeywordsTRANSFERASE / putative sugar kinases / Arabidopsis thaliana / ADP
Function / homology
Function and homology information


D-ribulokinase / D-ribulokinase activity / plastid / chloroplast / ATP binding / cytoplasm / cytosol
Similarity search - Function
Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / D-ribulose kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.492 Å
AuthorsXie, Y. / Li, M. / Chang, W.
CitationJournal: Plos One / Year: 2016
Title: Crystal Structures of Putative Sugar Kinases from Synechococcus Elongatus PCC 7942 and Arabidopsis Thaliana
Authors: Xie, Y. / Li, M. / Chang, W.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Data collection / Refinement description
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative xylulose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1842
Polymers47,7571
Non-polymers4271
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-3 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.527, 87.486, 53.361
Angle α, β, γ (deg.)90.00, 97.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative xylulose kinase / Xylulose kinase like protein / Xylulose kinase-1


Mass: 47756.930 Da / Num. of mol.: 1 / Fragment: UNP residues 43-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: XK-1, At2g21370 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8L794
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 73256 / % possible obs: 96.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.37
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 5.26 / % possible all: 90

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.492→42.835 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.65
RfactorNum. reflection% reflection
Rfree0.172 3432 4.85 %
Rwork0.1434 --
obs0.1448 70724 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.492→42.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 27 292 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143357
X-RAY DIFFRACTIONf_angle_d1.4534566
X-RAY DIFFRACTIONf_dihedral_angle_d13.0341226
X-RAY DIFFRACTIONf_chiral_restr0.067511
X-RAY DIFFRACTIONf_plane_restr0.008583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4919-1.51240.21351350.13442470X-RAY DIFFRACTION89
1.5124-1.5340.18161180.12472643X-RAY DIFFRACTION95
1.534-1.55690.19261370.11412654X-RAY DIFFRACTION95
1.5569-1.58120.16821400.10852633X-RAY DIFFRACTION95
1.5812-1.60710.15311330.10682647X-RAY DIFFRACTION95
1.6071-1.63490.1531330.10572638X-RAY DIFFRACTION96
1.6349-1.66460.1751340.10632694X-RAY DIFFRACTION95
1.6646-1.69660.15171350.11262651X-RAY DIFFRACTION96
1.6966-1.73120.18521360.11812670X-RAY DIFFRACTION96
1.7312-1.76890.16271140.11882721X-RAY DIFFRACTION96
1.7689-1.810.16661380.1222636X-RAY DIFFRACTION96
1.81-1.85530.17341430.11882709X-RAY DIFFRACTION97
1.8553-1.90550.16951240.1252733X-RAY DIFFRACTION97
1.9055-1.96150.17671410.12532666X-RAY DIFFRACTION97
1.9615-2.02480.15461500.12982701X-RAY DIFFRACTION98
2.0248-2.09720.17031410.12972730X-RAY DIFFRACTION98
2.0972-2.18120.1671400.13162729X-RAY DIFFRACTION98
2.1812-2.28040.17861460.14442730X-RAY DIFFRACTION98
2.2804-2.40060.17261470.15062724X-RAY DIFFRACTION98
2.4006-2.5510.18281450.15252749X-RAY DIFFRACTION98
2.551-2.7480.16471430.16312762X-RAY DIFFRACTION99
2.748-3.02440.1811300.17252752X-RAY DIFFRACTION99
3.0244-3.46190.18151490.16622772X-RAY DIFFRACTION99
3.4619-4.3610.171540.15142735X-RAY DIFFRACTION98
4.361-42.85310.16451260.15782743X-RAY DIFFRACTION96

+
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