[English] 日本語
Yorodumi
- PDB-1glf: CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1glf
TitleCRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION
ComponentsPROTEIN (GLYCEROL KINASE)
KeywordsTRANSFERASE / ALLOSTERY / COOPERATIVITY / GLYCEROL KINASE
Function / homology
Function and homology information


glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / DNA damage response / zinc ion binding / ATP binding / identical protein binding ...glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / DNA damage response / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Glycerol kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsFeese, M.D. / Faber, H.R. / Bystrom, C.E. / Pettigrew, D.W. / Remington, S.J.
Citation
Journal: Structure / Year: 1998
Title: Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation.
Authors: Feese, M.D. / Faber, H.R. / Bystrom, C.E. / Pettigrew, D.W. / Remington, S.J.
#1: Journal: J.Bacteriol. / Year: 1996
Title: A Single Amino Acid Change in Escherichia Coli Glycerol Kinase Abolishes Glucose Control of Glycerol Utilization in Vivo
Authors: Pettigrew, D.W. / Liu, W.Z. / Holmes, C. / Meadow, N.D. / Roseman, S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Cation Promoted Association (Cpa) of a Regulatory and Target Protein is Controlled by Protein Phosphorylation
Authors: Feese, M.D. / Pettigrew, D.W. / Meadow, N.D. / Roseman, S. / Remington, S.J.
#3: Journal: Biochemistry / Year: 1994
Title: Escherichia Coli Glycerol Kinase: Role of a Tetramer Interface in Regulation by Fructose-1,6-Bisphosphate and Phoshotransferase System Regulatory Protein Iiiglc
Authors: Liu, W.Z. / Faber, H.R. / Feese, M.D. / Remington, S.J. / Pettigrew, D.W.
#4: Journal: Science / Year: 1993
Title: Structure of the Regulatory Complex of Escherichia Coli III==Glc== with Glycerol Kinase
Authors: Hurley, J.H. / Faber, H.R. / Worthylake, D. / Meadow, N.D. / Roseman, S. / Pettigrew, D.W. / Remington, S.J.
History
DepositionAug 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: PROTEIN (GLYCEROL KINASE)
Y: PROTEIN (GLYCEROL KINASE)
Z: PROTEIN (GLYCEROL KINASE)
X: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,91714
Polymers224,6494
Non-polymers2,26710
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-79 kcal/mol
Surface area64590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.100, 117.400, 108.400
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
PROTEIN (GLYCEROL KINASE)


Mass: 56162.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GLYCEROL ADENOSINE DIPHOSPHATE ORTHOPHOSPHATE / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLPK / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F3, glycerol kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Faber, H.R., (1989) J. Mol. Biol., 207, 637. / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-30 mg/mlprotein1drop
250 mMsodium potassium phosphate1drop
310 mMglycerol1drop
42 mMbeta-mercaptoethanol1drop
5300-500 mM1reservoirNaCl
620 %(w/w)PEG15501reservoirPEG1550 to 20000
750 mMsodium potassium phosphate1reservoir
8100 mMADP1drop

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Aug 1, 1990
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→20 Å / Num. obs: 58942 / % possible obs: 84 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 2.62 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 2 / Redundancy: 3 % / Num. measured all: 190143 / Biso Wilson estimate: 20.9 Å2

-
Processing

Software
NameVersionClassification
FRFSUM(WOLFGANG KABSCH)model building
UNPUBLISHEDPROGRAMS BY SJRmodel building
TNT5F-6refinement
SDMSdata reduction
SDMSdata scaling
FRFSUM(WOLFGANG KABSCH)phasing
UNPUBLISHEDPROGRAMS BY SJRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GLA

1gla


Resolution: 2.62→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: BSOL AND KSOL SET BY USER GLYCEROL KINASE EXISTS AT PHYSIOLOGICAL CONCENTRATIONS IN AN EQUILIBRIUM BETWEEN FUNCTIONAL DIMERS AND TETRAMERS. THE CRYSTAL ASYMMETRIC UNIT CONTAINS A TETRAMER OF ...Details: BSOL AND KSOL SET BY USER GLYCEROL KINASE EXISTS AT PHYSIOLOGICAL CONCENTRATIONS IN AN EQUILIBRIUM BETWEEN FUNCTIONAL DIMERS AND TETRAMERS. THE CRYSTAL ASYMMETRIC UNIT CONTAINS A TETRAMER OF GLYCEROL KINASE WITH NEARLY EXACT 222 POINT-GROUP SYMMETRY, UNLIKE THE PREVIOUSLY SUBMITTED GLYCEROL KINASE - FACTOR IIIGLC COMPLEX IN WHICH THE 222 POINT GROUP SYMMETRY WAS CRYSTALLOGRAPHICALLY ENFORCED
RfactorNum. reflection% reflection
Rwork0.146 --
obs-58942 84 %
Solvent computationSolvent model: TNT SOLVENT MODELING / Bsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.62→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15639 0 142 200 15981
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02161031.5
X-RAY DIFFRACTIONt_angle_deg2.99217753
X-RAY DIFFRACTIONt_dihedral_angle_d20.90495350
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0174162.2
X-RAY DIFFRACTIONt_gen_planes0.01923357.7
X-RAY DIFFRACTIONt_it9.87159591
X-RAY DIFFRACTIONt_nbd0.03493920
Software
*PLUS
Name: TNT / Version: 5F-6 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.9040
X-RAY DIFFRACTIONt_planar_d0.0172.2
X-RAY DIFFRACTIONt_plane_restr0.0197.7

+
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