[English] 日本語
Yorodumi
- PDB-6r2n: Crystal structure of KlGlk1 glucokinase from Kluyveromyces lactis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r2n
TitleCrystal structure of KlGlk1 glucokinase from Kluyveromyces lactis
ComponentsGlucokinase-1
KeywordsTRANSFERASE / Kluyveromyces lactis / glucokinase / sugar metabolism
Function / homology
Function and homology information


glycolytic fermentation / glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / glucose binding / fructose 6-phosphate metabolic process / intracellular glucose homeostasis ...glycolytic fermentation / glucokinase / mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / glucose binding / fructose 6-phosphate metabolic process / intracellular glucose homeostasis / glycolytic process / ATP binding
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Glucokinase-1
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsZak, K. / Wator, E. / Grudnik, P.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2015/19/D/NZ1/02009 Poland
CitationJournal: Int J Mol Sci / Year: 2019
Title: Crystal Structure of Kluyveromyces lactis Glucokinase ( Kl Glk1).
Authors: Zak, K.M. / Kalinska, M. / Wator, E. / Kuska, K. / Krutyholowa, R. / Dubin, G. / Popowicz, G.M. / Grudnik, P.
History
DepositionMar 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)160,24415
Polymers159,4813
Non-polymers76312
Water3,531196
1
A: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6579
Polymers53,1601
Non-polymers4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3464
Polymers53,1601
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2402
Polymers53,1601
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.011, 122.771, 360.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-601-

HOH

21C-634-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 4 or (resid 5...
21(chain B and (resid 3 through 25 or resid 27...
31(chain C and (resid 3 through 7 or (resid 8...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPRO(chain A and (resid 3 through 4 or (resid 5...AA3 - 42 - 3
12LYSLYSLYSLYS(chain A and (resid 3 through 4 or (resid 5...AA54
13SERSERTYRTYR(chain A and (resid 3 through 4 or (resid 5...AA2 - 4811 - 475
14SERSERTYRTYR(chain A and (resid 3 through 4 or (resid 5...AA2 - 4811 - 475
15SERSERTYRTYR(chain A and (resid 3 through 4 or (resid 5...AA2 - 4811 - 475
16SERSERTYRTYR(chain A and (resid 3 through 4 or (resid 5...AA2 - 4811 - 475
21ASPASPSERSER(chain B and (resid 3 through 25 or resid 27...BB3 - 252 - 24
22LEULEUGLUGLU(chain B and (resid 3 through 25 or resid 27...BB27 - 3626 - 35
23LYSLYSLYSLYS(chain B and (resid 3 through 25 or resid 27...BB3736
24SERSERTYRTYR(chain B and (resid 3 through 25 or resid 27...BB2 - 4811 - 475
25SERSERTYRTYR(chain B and (resid 3 through 25 or resid 27...BB2 - 4811 - 475
26SERSERTYRTYR(chain B and (resid 3 through 25 or resid 27...BB2 - 4811 - 475
27SERSERTYRTYR(chain B and (resid 3 through 25 or resid 27...BB2 - 4811 - 475
31ASPASPTHRTHR(chain C and (resid 3 through 7 or (resid 8...CC3 - 72 - 6
32LYSLYSALAALA(chain C and (resid 3 through 7 or (resid 8...CC8 - 97 - 8
33SERSERTYRTYR(chain C and (resid 3 through 7 or (resid 8...CC2 - 4811 - 475

-
Components

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


Mass: 53160.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: GLK1, KLLA0C01155g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6CUZ3, glucokinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.15 M KBr and 30 % PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.596→49.08 Å / Num. obs: 69999 / % possible obs: 99.58 % / Redundancy: 2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Rrim(I) all: 0.065 / Net I/σ(I): 13.6
Reflection shellResolution: 2.596→2.689 Å / Redundancy: 2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6782 / CC1/2: 0.528 / Rpim(I) all: 0.482 / Rrim(I) all: 0.681 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o8M

3o8m


Resolution: 2.596→49.077 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.2431 2108 1.58 %
Rwork0.2045 --
obs0.2051 69999 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 259.93 Å2 / Biso mean: 83.3925 Å2 / Biso min: 27.69 Å2
Refinement stepCycle: final / Resolution: 2.596→49.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10914 0 111 196 11221
Biso mean--96.15 53.66 -
Num. residues----1423
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5961X-RAY DIFFRACTION8.512TORSIONAL
12B5961X-RAY DIFFRACTION8.512TORSIONAL
13C5961X-RAY DIFFRACTION8.512TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5962-2.65660.38651370.37788563870095
2.6566-2.7230.30771380.34478539867798
2.723-2.79660.29451410.293488689009100
2.7966-2.87890.26661430.272188288971100
2.8789-2.97180.29241420.263588799021100
2.9718-3.0780.27611400.267188809020100
3.078-3.20120.28521400.247388508990100
3.2012-3.34690.2511430.220588168959100
3.3469-3.52330.30731360.23158718885499
3.5233-3.74390.25491430.20678815895899
3.7439-4.03290.2081400.18248648878898
4.0329-4.43850.22271410.16138853899499
4.4385-5.08020.21161430.152787428885100
5.0802-6.39830.21181390.194288318970100
6.3983-49.08560.21451420.1718777891999
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)
11.4523-0.21860.70791.09580.04791.173-0.0348-0.0044-0.29830.1160.11040.01190.10280.0152-0.07810.2958-0.00960.04540.31240.01760.462613.681341.1743181.1031
22.12870.75440.18921.245-0.18171.5490.00070.30710.22250.2306-0.0102-0.0382-0.60610.2527-0.00280.7963-0.235-0.10550.63970.08680.482114.83050.4193215.3348
30.662-0.1046-0.04321.73940.13.0010.1678-0.2209-0.07860.44220.15040.09560.1307-0.6058-0.28570.7409-0.2203-0.11040.75430.14810.524946.57838.9541241.3224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 481)A2 - 481
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 481)B2 - 481
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 481)C2 - 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