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- PDB-3o08: Crystal structure of dimeric KlHxk1 in crystal form I -

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Basic information

Entry
Database: PDB / ID: 3o08
TitleCrystal structure of dimeric KlHxk1 in crystal form I
ComponentsHexokinase
KeywordsTRANSFERASE / RNaseH-like fold / Hexokinase / Glycolysis / Glucose repression / ATP binding / Mig1 binding
Function / homology
Function and homology information


mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion ...mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol
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 / Nucleotidyltransferase; domain 5 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKuettner, E.B. / Kettner, K. / Keim, A. / Kriegel, T.M. / Strater, N.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Crystal Structure of Hexokinase KlHxk1 of Kluyveromyces lactis: A MOLECULAR BASIS FOR UNDERSTANDING THE CONTROL OF YEAST HEXOKINASE FUNCTIONS VIA COVALENT MODIFICATION AND OLIGOMERIZATION.
Authors: Kuettner, E.B. / Kettner, K. / Keim, A. / Svergun, D.I. / Volke, D. / Singer, D. / Hoffmann, R. / Muller, E.C. / Otto, A. / Kriegel, T.M. / Strater, N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and preliminary X-ray diffraction studies of hexokinase KlHxk1 from Kluyveromyces lactis
Authors: Kuettner, E.B. / Kriegel, T.M. / Keim, A. / Naumann, M. / Strater, N.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,66525
Polymers107,3442
Non-polymers2,32123
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-274 kcal/mol
Surface area39030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.692, 113.219, 91.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hexokinase


Mass: 53672.062 Da / Num. of mol.: 2
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-delta-rag5 / References: UniProt: P33284, hexokinase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 1MICROL RESERVOIR + 1MICROL PROTEIN; RESERVOIR: 2.5M AMMONIA SULFATE, 0.1M CHES PH 9.4, PROTEIN: 10MG/ML KLHXK1, 10MM TRIS PH 7.4, 1MM EDTA, 1MM DTT, 0.5MM PMSF, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.894 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 2005 / Details: Si, coated with 200 layers of Mo/Si
RadiationMonochromator: Si - 111 triangular crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.894 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 69759 / Num. obs: 69639 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 31.3 Å2 / Rsym value: 0.07 / Net I/σ(I): 22
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 4.9 / Num. unique all: 5044 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IG8

1ig8


Resolution: 2→29.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.753 / SU ML: 0.126 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FULL B FACTORS AND ANISO RECORDS WERE COMPUTED BY CCP4 PROGRAMM TLSANL.
RfactorNum. reflection% reflectionSelection details
Rfree0.24366 1033 1.5 %RANDOM
Rwork0.18501 ---
obs0.18587 68555 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--1.58 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7391 0 123 400 7914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0227654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.99510378
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91225.229327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.828151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9381531
X-RAY DIFFRACTIONr_chiral_restr0.1460.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215655
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.33334715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.10947621
X-RAY DIFFRACTIONr_scbond_it5.262939
X-RAY DIFFRACTIONr_scangle_it6.97492757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 75 -
Rwork0.194 4944 -
obs--98.92 %
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)
11.0344-0.09020.24571.96171.38292.276-0.06840.01770.09270.1717-0.05370.0353-0.1171-0.12110.12220.1126-0.01420.00550.02420.00660.104652.947124.858957.9714
23.54231.21420.98081.20640.83813.7181-0.13860.06740.1617-0.05760.0315-0.084-0.18780.28850.10710.07580.02670.00980.1010.01340.097174.335214.701639.3399
31.45810.3809-1.29090.9217-1.50415.6224-0.16270.1613-0.0311-0.0543-0.2185-0.0620.1560.49440.38120.0189-0.0136-0.00190.12540.04120.128684.23827.242480.5412
40.732-0.6360.61813.7748-2.47095.9963-0.17560.09840.19150.39150.0077-0.0053-0.9914-0.31160.16780.22120.0966-0.030.1557-0.01810.166763.87419.42699.0166
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 76
2X-RAY DIFFRACTION1A210 - 456
3X-RAY DIFFRACTION2A77 - 209
4X-RAY DIFFRACTION2A457 - 485
5X-RAY DIFFRACTION3B2 - 76
6X-RAY DIFFRACTION3B210 - 456
7X-RAY DIFFRACTION4B77 - 209
8X-RAY DIFFRACTION4B457 - 485

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