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- PDB-3o80: Crystal structure of monomeric KlHxk1 in crystal form IX (open state) -

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Basic information

Entry
Database: PDB / ID: 3o80
TitleCrystal structure of monomeric KlHxk1 in crystal form IX (open state)
ComponentsHexokinase
KeywordsTRANSFERASE / RNASEH-LIKE FOLD / HEXOKINASE / GLYCOLYSIS / GLUCOSE REPRESSION / ATP BINDING / MIG1 BINDING
Function / homology
Function and homology information


hexose metabolic process / hexokinase / fructokinase activity / glucokinase activity / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Hexokinase
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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
DepositionAug 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6843
Polymers53,6721
Non-polymers1,0122
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.346, 233.904, 49.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hexokinase /


Mass: 53672.062 Da / Num. of mol.: 1
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 61.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.5microL reservoir + 0.5microL protein, reservoir: 1.6M triammonium citrate pH 6, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 2mM AMPPCP, crystal soaked in ...Details: 0.5microL reservoir + 0.5microL protein, reservoir: 1.6M triammonium citrate pH 6, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 2mM AMPPCP, crystal soaked in 50mM AMPPNP, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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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: Apr 30, 2008
Details: 1st mirror: Silicon, active surface 50 nm Rh-coated; 2nd mirror: Glas, active s urface 50 nm Rh-coated
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: 2.18→30 Å / Num. all: 36671 / Num. obs: 36453 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 15.2
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2656 / Rsym value: 0.506 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O08
Resolution: 2.18→29.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 11.105 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R Free: 0.181 / 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
Rfree0.25074 1136 3.1 %RANDOM
Rwork0.19848 ---
obs0.20009 35317 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.011 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.92 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.18→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 46 99 3796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9925126
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.225.305164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2515657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5531515
X-RAY DIFFRACTIONr_chiral_restr0.1310.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212823
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_it2.31532325
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.43443759
X-RAY DIFFRACTIONr_scbond_it6.04261452
X-RAY DIFFRACTIONr_scangle_it8.60291367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 80 -
Rwork0.255 2559 -
obs--99.89 %
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)
10.38940.4272-0.00972.86811.41921.4324-0.04180.0160.0406-0.06710.01740.02360.00620.04440.02430.0347-0.03-0.00120.04760.02530.043821.695640.80651.4814
23.8675-0.9914-1.86732.6076-0.52723.4198-0.0686-0.65880.32040.30140.2056-0.23130.03760.458-0.1370.09350.0147-0.0240.1267-0.06090.037217.904211.492912.3025
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

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