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- PDB-4jax: Crystal structure of dimeric KlHxk1 in crystal form X -

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Basic information

Entry
Database: PDB / ID: 4jax
TitleCrystal structure of dimeric KlHxk1 in crystal form X
ComponentsHexokinase
KeywordsTRANSFERASE / ribonuclease H-fold / hexokinase / ATP binding / sugar binding / Mig1 binding / phosphorylation
Function / homology
Function and homology information


hexose metabolic process / hexokinase / fructokinase activity / glucokinase activity / glucose binding / intracellular glucose homeostasis / glycolytic process / ATP binding
Similarity search - Function
Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. ...Helix Hairpins - #1250 / 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 / Helix Hairpins / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hexokinase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsKuettner, E.B. / Strater, N. / Kettner, K. / Otto, A. / Lilie, H. / Golbik, R.P. / Kriegel, T.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: In vivo phosphorylation and in vitro autophosphorylation-inactivation of Kluyveromyces lactis hexokinase KlHxk1.
Authors: Kettner, K. / Kuettner, E.B. / Otto, A. / Lilie, H. / Golbik, R.P. / Strater, N. / Kriegel, T.M.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexokinase
B: Hexokinase
C: Hexokinase
D: Hexokinase
E: Hexokinase
F: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,86431
Polymers322,5126
Non-polymers2,35125
Water6,377354
1
A: Hexokinase
D: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,54013
Polymers107,5042
Non-polymers1,03611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hexokinase
C: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,25510
Polymers107,5042
Non-polymers7518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Hexokinase
F: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0688
Polymers107,5042
Non-polymers5646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3167
Polymers53,7521
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9393
Polymers53,7521
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
C: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3167
Polymers53,7521
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
D: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2246
Polymers53,7521
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
E: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2216
Polymers53,7521
Non-polymers4695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
F: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8472
Polymers53,7521
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.810, 178.300, 216.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailschains A+D form a dimer / chains B+C form a dimer / chains E+F form a dimer

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Components

#1: Protein
Hexokinase /


Mass: 53752.043 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: CBS2359/152 / Gene: KLLA0D11352g, RAG5 / Plasmid: pTSRAG5 / Production host: Kluyveromyces lactis (yeast) / Strain (production host): JA6 rag5 / References: UniProt: P33284, hexokinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1 microliter protein (7.8 mg/ml KlHxk1 in buffer (10 mM Tris, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, pH 7.4)) + 1 microliter reservoir (2.2 M (NH4)2HPO4, 0.1 M Tris pH 8.5), micro seeding, VAPOR ...Details: 1 microliter protein (7.8 mg/ml KlHxk1 in buffer (10 mM Tris, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, pH 7.4)) + 1 microliter reservoir (2.2 M (NH4)2HPO4, 0.1 M Tris pH 8.5), micro seeding, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 19, 2008 / Details: mirror
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.26→29.85 Å / Num. all: 191251 / Num. obs: 190903 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 47.2 Å2 / Rsym value: 0.049 / Net I/σ(I): 24.25
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.84 / Num. unique all: 14012 / Rsym value: 0.502 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A of PDB entry 3O1W

3o1w


Resolution: 2.26→29.602 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.873 / SU ML: 0.154 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT, temperature factors of atoms are full B values (residual+TLS part)
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1912 1 %RANDOM
Rwork0.2003 ---
obs0.2007 190815 99.83 %-
all-191035 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.58 Å2 / Biso mean: 49.6244 Å2 / Biso min: 18.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å20 Å2
2---0.25 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.26→29.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21972 0 133 354 22459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922531
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.98430519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82852813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15525.261977
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97153957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8531590
X-RAY DIFFRACTIONr_chiral_restr0.0890.23413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116792
X-RAY DIFFRACTIONr_mcbond_it3
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4
X-RAY DIFFRACTIONr_scbond_it6
X-RAY DIFFRACTIONr_scangle_it9
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 148 -
Rwork0.264 13772 -
all-13920 -
obs-13772 99.96 %
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)
12.28670.32571.14534.63784.58055.9880.02310.1475-0.2281-0.0284-0.0610.33030.1503-0.10870.03790.1066-0.0050.03460.0224-0.01020.2544-52.16596.2941-40.5379
23.2586-1.48520.1661.74990.4221.7358-0.1018-0.02460.04520.0680.1139-0.0603-0.03230.1247-0.01210.14970.0345-0.00280.1245-0.12660.1484-23.367619.814-20.9905
30.8146-0.2001-0.0251.82260.96811.4734-0.0408-0.0467-0.12350.12870.07420.06170.21010.0387-0.03340.11370.01250.00960.0316-0.05240.1652-40.73977.3136-39.1029
42.70040.36091.44282.10560.97772.6736-0.22740.18420.3259-0.13920.09080.0309-0.19840.28130.13660.1036-0.01370.0140.048-0.02290.1868-39.952124.6047-36.3166
52.1231-0.22630.46493.6337-4.05096.4478-0.1014-0.2242-0.371-0.0978-0.1551-0.25410.19260.73560.25650.23460.05660.03640.23470.00230.20330.045922.677816.1813
63.2809-1.356-0.71723.70211.96443.3273-0.1079-0.0147-0.06740.2148-0.25720.4978-0.2925-0.36330.36510.47570.0673-0.02530.1231-0.10330.1555-25.180846.20010.6061
70.7942-0.0483-0.13881.3387-1.13242.7354-0.06210.0793-0.0981-0.16890.09640.04870.04780.079-0.03430.2472-0.0096-0.01690.038-0.02480.1221-10.346227.328815.5891
83.2072-1.7381.41982.9183-1.89543.6603-0.2402-0.10030.31370.26-0.0023-0.2443-0.76490.34080.24250.4194-0.108-0.03530.0835-0.04350.1148-5.467843.773412.334
925.3585-6.0696-13.1491.46493.15756.82750.2778-0.31490.5679-0.16170.0493-0.1362-0.23510.1995-0.32710.6346-0.0409-0.09380.83350.15830.798-35.278759.850117.5583
102.0231-0.24450.42892.5042-0.39670.78430.0164-0.24840.05680.2583-0.0338-0.0688-0.0405-0.05090.01740.1845-0.00170.03970.075-0.01070.0178-18.608351.473648.0934
113.41511.0268-0.3946.62230.25673.8470.2029-0.4791-0.42630.6405-0.2137-0.0631-0.072-0.10220.01070.33360.0166-0.07810.14530.11770.1411-11.661633.398959.7467
123.69-1.21821.62422.1779-0.47741.96120.1718-0.1347-0.23840.0687-0.06690.29460.2068-0.2648-0.10490.1678-0.03440.04510.0472-0.01320.0893-24.858653.846742.6075
132.15560.24981.16841.75670.21431.7086-0.13530.00840.4407-0.1688-0.0751-0.0904-0.4053-0.10790.21040.37490.0769-0.00650.09010.01050.2493-14.636823.2549-63.876
142.35440.3116-1.51225.0905-0.53845.6817-0.11930.1601-0.1162-0.4522-0.14510.0358-0.2039-0.54370.26450.39780.0269-0.10570.1634-0.05850.1552-28.45279.6857-78.9255
152.12580.38480.39312.18260.34262.1421-0.11520.2730.0923-0.5249-0.011-0.1123-0.1795-0.19380.12620.45210.087-0.04370.15670.03290.1653-21.621920.5059-77.7858
161.6569-0.85891.51641.5756-1.03842.6353-0.07530.03610.2623-0.1987-0.0465-0.1374-0.2710.01370.12170.25690.0321-0.01180.0462-0.02760.2063-8.973419.7546-57.1524
171.57030.16010.05413.1820.79631.87330.06540.0685-0.2807-0.3539-0.22710.4560.4158-0.23470.16170.3209-0.0659-0.01780.16070.02180.2333-28.295965.5429-83.8705
183.19450.05170.14214.3147-1.02892.9936-0.0004-0.3756-0.17950.1743-0.1640.01970.2769-0.19310.16440.1335-0.06640.04580.14750.02030.0926-20.135182.117-67.0279
191.7191-0.8673-0.74424.39781.352.9379-0.0048-0.1756-0.1808-0.0567-0.18630.02490.66740.01260.19110.3771-0.10070.02470.13080.07610.2016-24.901458.9527-81.6243
201.2434-0.6891-0.60174.01291.55293.50210.22730.1775-0.0454-0.8193-0.313-0.02820.3107-0.12050.08570.4692-0.0077-0.00960.14610.06750.1934-23.991163.1854-92.8144
213.31530.71872.33972.38721.984.4113-0.0090.22510.2526-0.29790.18680.2782-0.1701-0.3601-0.17780.2819-0.0807-0.00960.24140.19370.3042-15.2379102.2927-111.5387
225.189-1.76780.23775.3724-2.0635.65580.06590.4327-0.8869-0.6286-0.14010.72931.03160.31950.07420.7888-0.16140.00090.6001-0.15340.4822-21.081167.6434-124.0952
2312.1049-5.4652-7.52252.47343.38934.68530.52760.38980.8294-0.2224-0.1613-0.3879-0.2531-0.1221-0.36631.1944-0.2498-0.11881.69070.4450.6643-9.112280.2581-131.4421
241.62760.28250.57871.37530.36422.7040.03040.3443-0.0445-0.41080.01030.22540.2285-0.3286-0.04070.3641-0.088-0.02390.23810.07790.2087-15.854489.9054-112.4379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 65
2X-RAY DIFFRACTION2A66 - 209
3X-RAY DIFFRACTION3A210 - 421
4X-RAY DIFFRACTION4A422 - 484
5X-RAY DIFFRACTION5B13 - 65
6X-RAY DIFFRACTION6B66 - 209
7X-RAY DIFFRACTION7B210 - 409
8X-RAY DIFFRACTION8B410 - 484
9X-RAY DIFFRACTION9C11 - 19
10X-RAY DIFFRACTION10C20 - 118
11X-RAY DIFFRACTION11C119 - 208
12X-RAY DIFFRACTION12C209 - 485
13X-RAY DIFFRACTION13D13 - 115
14X-RAY DIFFRACTION14D116 - 173
15X-RAY DIFFRACTION15D174 - 255
16X-RAY DIFFRACTION16D256 - 485
17X-RAY DIFFRACTION17E16 - 114
18X-RAY DIFFRACTION18E115 - 207
19X-RAY DIFFRACTION19E208 - 329
20X-RAY DIFFRACTION20E330 - 485
21X-RAY DIFFRACTION21F15 - 71
22X-RAY DIFFRACTION22F72 - 157
23X-RAY DIFFRACTION23F158 - 189
24X-RAY DIFFRACTION24F190 - 485

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