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- PDB-6r2n: Crystal structure of KlGlk1 glucokinase from Kluyveromyces lactis -

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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


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; 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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