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- PDB-9f3n: Crystal structure of the intermediate open state of apo Kluyverom... -

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Basic information

Entry
Database: PDB / ID: 9f3n
TitleCrystal structure of the intermediate 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: 2.65 Å
AuthorsWeisse, R.H. / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,66512
Polymers107,6442
Non-polymers1,02010
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Equilibrium of a monomeric and a homodimeric state in solution. Exchange of key residues of the dimer interface essentially abolishes dimer formation.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint32 kcal/mol
Surface area38070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.664, 177.664, 90.026
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 2 through 42 or resid 49 through 481 or resid 482 through 495))

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_11SERSERTYRTYRAA2 - 4812 - 481
d_12MLIMLIMLIMLIAC501
d_13MLIMLIMLIMLIAD502
d_14MLIMLIMLIMLIAE503
d_15MLIMLIMLIMLIAF504
d_21SERSERCYSCYSBB2 - 422 - 42
d_22ASNASNTYRTYRBB49 - 48149 - 481
d_23MLIMLIMLIMLIBH501
d_24MLIMLIMLIMLIAG505
d_25MLIMLIMLIMLIBI502
d_26MLIMLIMLIMLIBJ503

NCS oper: (Code: givenMatrix: (-0.952998832407, 0.0343941654138, -0.301015392989), (0.00775998417209, -0.99043861993, -0.137735699061), (-0.302874574827, -0.133597835071, 0.943619950185)Vector: -79. ...NCS oper: (Code: given
Matrix: (-0.952998832407, 0.0343941654138, -0.301015392989), (0.00775998417209, -0.99043861993, -0.137735699061), (-0.302874574827, -0.133597835071, 0.943619950185)
Vector: -79.795107867, -88.3348061803, -18.4312936091)

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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.: 10 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: droplet: 1:1 mixture of protein and reservoir protein supplemented with: 9.9 mM DTT reservoir solution: 100 mM Na citrate pH 6.0 1.8 M Na malonate pH 5.7

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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: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.56→153.86 Å / Num. obs: 47188 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 73.29 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.2
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4587 / CC1/2: 0.302 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS1.dev.877-g8f078f0data reduction
Aimless0.5.31data scaling
MR-RosettaROSETTA 3.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→76.93 Å / SU ML: 0.4245 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 1889 4.01 %
Rwork0.2162 45226 -
obs0.2169 47115 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.39 Å2
Refinement stepCycle: LAST / Resolution: 2.65→76.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7492 0 70 17 7579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027699
X-RAY DIFFRACTIONf_angle_d0.509310407
X-RAY DIFFRACTIONf_chiral_restr0.03871181
X-RAY DIFFRACTIONf_plane_restr0.00511358
X-RAY DIFFRACTIONf_dihedral_angle_d12.63432829
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.73730627393 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.40471290.37173479X-RAY DIFFRACTION99.64
2.72-2.80.33581690.33273406X-RAY DIFFRACTION99.69
2.8-2.890.34531430.31363439X-RAY DIFFRACTION99.8
2.89-30.34431290.31233497X-RAY DIFFRACTION99.94
3-3.120.32981340.32573482X-RAY DIFFRACTION99.86
3.12-3.260.33891570.30623430X-RAY DIFFRACTION99.97
3.26-3.430.2821550.25543481X-RAY DIFFRACTION99.97
3.43-3.640.23041480.22563448X-RAY DIFFRACTION100
3.64-3.930.23341460.21423478X-RAY DIFFRACTION99.97
3.93-4.320.18861380.18023513X-RAY DIFFRACTION99.97
4.32-4.950.16821500.16293484X-RAY DIFFRACTION100
4.95-6.230.21171390.19443514X-RAY DIFFRACTION99.97
6.23-76.930.20971520.18013575X-RAY DIFFRACTION99.65
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)
13.381291219331.16872102919-0.4018473152652.15942640667-0.07019300122641.56521956383-0.1029947284140.1151628353160.0250244310052-0.0703758701020.2478528445750.1072779501140.129089942904-0.171903076071.06836421695E-50.703647971129-0.132231722004-0.09479535210240.6553487802110.04961162496030.543914634863-46.6288412493-62.65872881351.58645059315
21.11613981794-0.222804064216-0.0922552416841.782300038610.07346071143594.15315818211-0.09168686736850.161804485182-0.03604162696650.04884389522850.321808083693-0.2282972774-0.2410842232620.30459592608-3.90367856951E-50.802471675889-0.104900698710.04255653232090.755692323178-0.07468630645830.733955802665-32.5525530889-69.7733650799-21.2906578428
33.31409218325-0.1529352057741.482152263121.55668545952-0.2901545546392.20501587839-0.182410975561-0.06279126265030.3855013146160.2547270132720.0574991929576-0.0776071516209-0.289431101038-0.197512187662-5.29399345617E-60.6990097853910.0526195380014-0.06029450744140.6030735250.001770932661690.634663590121-38.5160756597-26.30377728665.53731114285
42.371566320880.557313539498-0.03732218344783.2834190146-1.50641157623.88211807979-0.3279416697010.09082222262250.0789943993342-0.01214576331910.150282185891-0.121022099675-0.17919352068-0.0403779836251-2.30849668755E-50.6963419460190.112187622808-0.1266797498050.6487563765470.08415077578840.782776614404-44.5881698764-16.7596806766-19.021639928
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resi 2:63 or resi 205:463)AA2 - 4632 - 456
22chain A and (resi 64:204 or resi 464:481)AA64 - 48157 - 474
33chain B and (resi 2:63 or resi 205:463)BG2 - 4632 - 462
44chain B and (resi 64:204 or resi 464:481)BG64 - 48163 - 480

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