[English] 日本語
Yorodumi
- PDB-3h46: Glycerol Kinase H232E with Glycerol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h46
TitleGlycerol Kinase H232E with Glycerol
ComponentsGlycerol kinase
KeywordsTRANSFERASE / glycerol / kinase / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / ATP binding
Similarity search - Function
FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / 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 ...FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / 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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYeh, J.I. / Kettering, R.D.
CitationJournal: Biochemistry / Year: 2009
Title: Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation
Authors: Yeh, J.I. / Kettering, R. / Saxl, R. / Bourand, A. / Darbon, E. / Joly, N. / Briozzo, P. / Deutscher, J.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Glycerol kinase
O: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1078
Polymers111,6072
Non-polymers5006
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: Glycerol kinase
O: Glycerol kinase
hetero molecules

X: Glycerol kinase
O: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,21516
Polymers223,2144
Non-polymers1,00112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12640 Å2
ΔGint-97 kcal/mol
Surface area67320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.677, 199.548, 56.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Glycerol kinase / / ATP:glycerol 3-phosphotransferase / Glycerokinase / GK


Mass: 55803.453 Da / Num. of mol.: 2 / Mutation: H232E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: glpK / Plasmid: pOXO4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: O34153, glycerol kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: HEPES, PEG 550 MME, ZnSO4, pH 6.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 100197 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.096 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.509 / % possible all: 81.4

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XUP

1xup


Resolution: 1.75→10 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 3
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4004 5 %RANDOM
Rwork0.194 ---
all0.196 79736 --
obs0.196 75732 71.99 %-
Displacement parametersBiso max: 66.45 Å2 / Biso mean: 25.631 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7758 0 30 193 7981
LS refinement shellResolution: 1.751→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 54 -
Rwork0.228 1155 -
all-1209 -
obs--15.33 %

+
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