[English] 日本語
Yorodumi
- PDB-9f3o: Crystal structure of the open state of apo Kluyveromyces lactis g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f3o
TitleCrystal structure of the open state of apo Kluyveromyces lactis glucokinase
ComponentsGlucokinase-1
KeywordsTRANSFERASE / sugar metabolism
Function / homology
Function and homology information


glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion ...glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol
Similarity search - Function
Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain
Similarity search - Domain/homology
MALONATE ION / Glucokinase-1
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsWeisse, R.H. / Kuettner, E.B. / Keim, A. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To be published
Title: Structural basis of hexose specificity and catalytic properties of Kluyveromyces lactis glucokinase KlGlk1
Authors: Weisse, R.H. / Kettner, K. / Lilie, H. / Funk, L. / Roedel, G. / Tittmann, K. / Strater, N. / Kriegel, T.M.
History
DepositionApr 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucokinase-1
B: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8484
Polymers107,6442
Non-polymers2042
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint8 kcal/mol
Surface area39390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.433, 116.433, 377.053
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 43 or resid 51 through 481 or resid 600))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERGLUGLUAA2 - 432 - 43
d_12GLYGLYTYRTYRAA51 - 48151 - 481
d_13MLIMLIMLIMLIAC600
d_21SERSERTYRTYRBB2 - 4812 - 481
d_22MLIMLIMLIMLIBD600

NCS oper: (Code: givenMatrix: (-0.629293243666, 0.106718722899, -0.769805902588), (0.156501699365, -0.952834149515, -0.260027501648), (-0.761247155378, -0.28410948189, 0.582910431137)Vector: -28. ...NCS oper: (Code: given
Matrix: (-0.629293243666, 0.106718722899, -0.769805902588), (0.156501699365, -0.952834149515, -0.260027501648), (-0.761247155378, -0.28410948189, 0.582910431137)
Vector: -28.544362831, -75.2482977553, -27.6734208333)

-
Components

#1: Protein Glucokinase-1 / Glucose kinase 1 / GLK-1 / Hexokinase GLK1


Mass: 53822.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: JA6 / Gene: GLK1, KLLA0C01155g / Production host: Kluyveromyces lactis (yeast) / Strain (production host): JA6 / References: UniProt: Q6CUZ3, glucokinase, hexokinase
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: droplet: 1:1 mixture of protein and reservoir protein supplemented with: 10 mM MgCl2 10 mM AMPPNP reservoir solution: 100 mM Na citrate (pH 3.0) 1.5 M Na malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.08→29.02 Å / Num. obs: 28489 / % possible obs: 98.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 70.484 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.9
Reflection shellResolution: 3.08→3.27 Å / Redundancy: 6.4 % / Num. unique obs: 4437 / CC1/2: 0.794 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSVERSION Feb 5, 2021 BUILT=20210205data reduction
XSCALEVERSION Feb 5, 2021 BUILT=20210205data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→29.02 Å / SU ML: 0.4436 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 1449 5.09 %
Rwork0.2134 27010 -
obs0.2151 28459 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.3 Å2
Refinement stepCycle: LAST / Resolution: 3.08→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7484 0 14 0 7498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217643
X-RAY DIFFRACTIONf_angle_d0.476310341
X-RAY DIFFRACTIONf_chiral_restr0.03741180
X-RAY DIFFRACTIONf_plane_restr0.00391341
X-RAY DIFFRACTIONf_dihedral_angle_d12.3482809
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.93058855299 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.190.42771430.38122510X-RAY DIFFRACTION94.45
3.19-3.320.3251470.28352683X-RAY DIFFRACTION99.47
3.32-3.470.30441560.27092643X-RAY DIFFRACTION99.26
3.47-3.650.29421420.26682701X-RAY DIFFRACTION99.23
3.65-3.880.23651460.22542672X-RAY DIFFRACTION98.88
3.88-4.180.25591360.21642687X-RAY DIFFRACTION98.74
4.18-4.60.21491450.19982698X-RAY DIFFRACTION98.27
4.6-5.260.21961540.18672707X-RAY DIFFRACTION98.28
5.26-6.610.25931360.22132781X-RAY DIFFRACTION98.25
6.61-29.020.21091440.16262928X-RAY DIFFRACTION96.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.542673011170.6333807171560.7849770592221.071792711820.8132301406382.84240555511-0.07338096250880.0741024980320.166064264950.08224537412090.1171673295390.249814771297-0.0398654082757-0.181508198347-0.01618889065790.6114622759350.06299549033130.03266119753360.4167722033430.04851506913020.631766979745-24.216-21.6990.131
22.683483712951.276826234090.6262265401322.500753890480.9240686909221.146423719970.1177180469760.111127730158-0.4161606102090.1730199498450.0170249940444-0.1580285220320.2447361045120.125619370669-0.1534490788770.7186907654680.0700215649922-0.1066346637130.507272364079-0.09828947269020.742376743075-15.241-58.074-3.579
32.36914720361-0.1526004137880.3571895039232.83834933071-0.4991597314143.95512695006-0.1640607882140.08158025809380.0331793560293-0.2717272920220.2012600062550.126442858244-0.123877083652-0.0211765177582-0.03937626493110.571684829318-0.0425635792438-0.1116205439070.553399213472-0.03797590412780.579391194356-24.465-16.216-29.595
41.31137407541-0.4202809290140.6738209301691.664417646520.6455779567913.195052086250.07953105193540.0628925170902-0.0756419999623-0.7062054251640.561541643376-0.439764351092-0.001500765632370.505966462179-0.6338971447651.14475814354-0.0756501691449-0.02410011935681.29524498641-0.2170976584741.143698267516.215-56.082-21.112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:61 OR RESID 205:463 ) )A2 - 61
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:61 OR RESID 205:463 ) )A205 - 463
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 2:61 OR RESID 205:463 ) )B2 - 61
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 2:61 OR RESID 205:463 ) )B205 - 463
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 62:204 OR RESID 464:481 ) )A62 - 204
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 62:204 OR RESID 464:481 ) )A464 - 481
7X-RAY DIFFRACTION4( CHAIN B AND ( RESID 62:204 OR RESID 464:481 ) )B62 - 204
8X-RAY DIFFRACTION4( CHAIN B AND ( RESID 62:204 OR RESID 464:481 ) )B464 - 481

+
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