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- PDB-3vpz: Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A -

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Basic information

Entry
Database: PDB / ID: 3vpz
TitleCrystal structure of glucokinase from Antarctic psychrotroph at 1.69A
ComponentsGlucokinase
KeywordsTRANSFERASE / GLUCOKINASE / COLD-ADAPTED
Function / homology
Function and homology information


glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding / cytosol
Similarity search - Function
: / Glucokinase / Glucokinase / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsOda, T. / Fuchita, N. / Motoshima, H. / Kawamoto, M. / Watanabe, K.
CitationJournal: To be Published
Title: Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A
Authors: Oda, T. / Fuchita, N. / Motoshima, H. / Kawamoto, M. / Watanabe, K.
History
DepositionMar 16, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase


Theoretical massNumber of molelcules
Total (without water)35,1321
Polymers35,1321
Non-polymers00
Water4,017223
1
A: Glucokinase

A: Glucokinase


Theoretical massNumber of molelcules
Total (without water)70,2632
Polymers70,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2980 Å2
ΔGint-18 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.610, 98.610, 59.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glucokinase


Mass: 35131.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas (bacteria) / Strain: AS-131 / Gene: glk / Production host: Escherichia coli (E. coli) / References: UniProt: H7CHS4, glucokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Trimethylamine N-oxide dihydrate, 20% PEGMME 2000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SAGA-LS / Beamline: BL07 / Wavelength: 1.1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 31, 2011
RadiationMonochromator: Si(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.69→19.39 Å / Num. obs: 36190 / % possible obs: 95.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.3
Reflection shellHighest resolution: 1.69 Å / % possible all: 95.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0117refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q18

1q18


Resolution: 1.69→18.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.54 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24801 1820 5 %RANDOM
Rwork0.20147 ---
obs0.20379 34364 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.076 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.69→18.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 0 223 2628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192457
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7831.9413342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2545321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.85224.717106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.68615373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.387159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0211881
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 98 -
Rwork0.315 1779 -
obs--70.38 %

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