[English] 日本語
Yorodumi
- PDB-3hj6: Structure of Halothermothrix orenii fructokinase (FRK) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hj6
TitleStructure of Halothermothrix orenii fructokinase (FRK)
ComponentsFructokinase
KeywordsTRANSFERASE / fructokinase / fructose / kinase / carbohydrate metabolism
Function / homology
Function and homology information


fructokinase / fructokinase activity
Similarity search - Function
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase - #30 / YefM-like fold - #20 / Helix Hairpins - #490 / YefM-like fold / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase ...UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase - #30 / YefM-like fold - #20 / Helix Hairpins - #490 / YefM-like fold / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Helix Hairpins / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsChua, T.K. / Seetharaman, J. / Kasprzak, J.M. / Ng, C. / Patel, B.K. / Love, C. / Bujnicki, J.M. / Sivaraman, J.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystal structure of a fructokinase homolog from Halothermothrix orenii
Authors: Chua, T.K. / Seetharaman, J. / Kasprzak, J.M. / Ng, C. / Patel, B.K. / Love, C. / Bujnicki, J.M. / Sivaraman, J.
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructokinase
B: Fructokinase


Theoretical massNumber of molelcules
Total (without water)72,5182
Polymers72,5182
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-8 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.446, 171.941, 46.598
Angle α, β, γ (deg.)90.00, 112.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fructokinase / / FRK


Mass: 36258.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H168 / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / References: UniProt: B8CZ52, fructokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHOR SAID THAT THIS SEQUENCE IS VARIANT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.34 % / Description: The file contains Friedel pairs. / Mosaicity: 1.096 °
Crystal growTemperature: 297.15 K / Method: evaporation / pH: 8.5
Details: 8% PEG4000, 0.8M LiCl2, 0.1M Tris-HCl, pH 8.5, EVAPORATION, temperature 297.15K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9790, 0.9794, 0.9600
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.961
ReflectionResolution: 2.8→50 Å / Num. all: 30770 / Num. obs: 30770 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.046 / Χ2: 1.627 / Net I/σ(I): 37.529
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.224 / Num. unique all: 3129 / Χ2: 0.893 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1846 6 %random
Rwork0.254 ---
all0.2541 30193 --
obs0.2541 27077 88.5 %-
Solvent computationBsol: 58.865 Å2
Displacement parametersBiso max: 91.37 Å2 / Biso mean: 40.411 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.084 Å20 Å21.221 Å2
2--2.613 Å20 Å2
3----4.696 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 0 142 4079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.59
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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