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- PDB-3o5b: Crystal structure of dimeric KlHxk1 in crystal form VII with gluc... -

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Basic information

Entry
Database: PDB / ID: 3o5b
TitleCrystal structure of dimeric KlHxk1 in crystal form VII with glucose bound (open state)
ComponentsHexokinase
KeywordsTRANSFERASE / RNASEH-LIKE FOLD / HEXOKINASE / GLYCOLYSIS / GLUCOSE REPRESSION / ATP BINDING / MIG1 BINDING
Function / homology
Function and homology information


hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / glucose binding / cellular glucose homeostasis / glycolytic process / ATP binding
Similarity search - Function
Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase domain profile. / Hexokinase / Hexokinase / Hexokinase, C-terminal / Hexokinase, N-terminal / Hexokinase, binding site ...Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain signature. / Hexokinase domain profile. / Hexokinase / Hexokinase / Hexokinase, C-terminal / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase / 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
beta-D-glucopyranose / Hexokinase
Similarity search - Component
Biological speciesKluyveromyces lactis (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 27, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)107,9937
Polymers107,3442
Non-polymers6495
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.140, 122.200, 92.300
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 (unknown) / Strain: CBS2359/152 / Gene: KLLA0D11352g, RAG5 / Plasmid: pTSRAG5 / Production host: Kluyveromyces lactis (unknown) / Strain (production host): JA6-delta-rag5 / References: UniProt: P33284, hexokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1microL reservoir + 1microL protein, reservoir: 18% PEG6000, 0.9M LiCl, 2mM MgCl2, 0.1M Bicine pH 9.0, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, VAPOR ...Details: 1microL reservoir + 1microL protein, reservoir: 18% PEG6000, 0.9M LiCl, 2mM MgCl2, 0.1M Bicine pH 9.0, 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jun 19, 2009 / Details: Bent, vertically focussing
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 79077 / Num. obs: 78731 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 38.3 Å2 / Rsym value: 0.035 / Net I/σ(I): 28.4
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.87 / Num. unique all: 5724 / Rsym value: 0.492 / % possible all: 99.2

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O08
Resolution: 1.97→29.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.868 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.161 / 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
Rfree0.25506 1153 1.5 %RANDOM
Rwork0.20437 ---
obs0.20511 77579 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.129 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2--3.38 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7443 0 39 353 7835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.98410366
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26325.227331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4011532
X-RAY DIFFRACTIONr_chiral_restr0.1150.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215720
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_it2.8374.54756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.89667690
X-RAY DIFFRACTIONr_scbond_it6.62992892
X-RAY DIFFRACTIONr_scangle_it8.65413.52673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 87 -
Rwork0.29 5610 -
obs--99.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.55160.56420.13531.30060.70292.4754-0.19640.2117-0.1449-0.17650.1128-0.03880.3383-0.02610.08360.1444-0.04770.02590.0362-0.00030.14182.6709-24.4836-13.2831
22.9365-1.1952-0.66641.8767-0.5612.6107-0.1387-0.1759-0.0402-0.00320.0169-0.16920.18830.25030.12180.07770.0234-0.00250.03060.0030.114425.0323-15.85395.8149
31.7135-0.50642.37250.3644-0.62396.4876-0.27190.30460.08070.0402-0.0374-0.0206-0.30640.62950.30920.0853-0.11110.00180.18250.02410.133435.1853-8.092-35.0681
41.59180.3576-0.74782.883-0.81134.8119-0.0754-0.0227-0.4093-0.1213-0.06770.02530.8289-0.19430.14310.2193-0.12470.01540.2741-0.04560.163614.9578-21.5633-54.666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION1A210 - 456
3X-RAY DIFFRACTION2A77 - 209
4X-RAY DIFFRACTION2A457 - 485
5X-RAY DIFFRACTION3B1 - 76
6X-RAY DIFFRACTION3B210 - 456
7X-RAY DIFFRACTION4B77 - 209
8X-RAY DIFFRACTION4B457 - 485

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