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- PDB-5f11: Crystal structure of Fructokinase from Vibrio cholerae O395 in fr... -

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Database: PDB / ID: 5f11
TitleCrystal structure of Fructokinase from Vibrio cholerae O395 in fructose bound form
KeywordsTRANSFERASE / kinase / fructose / sodium
Function / homology
Function and homology information

fructokinase / fructokinase activity / nucleotide binding
Similarity search - Function
Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-fructofuranose / Fructokinase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
AuthorsPaul, R. / Nath, S. / Sen, U.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Atomic Energy, Govt. of India India
Journal: To Be Published
Title: Crystal structure of Fructokinase from Vibrio cholerae O395 in apo form
Authors: Paul, R. / Nath, S. / Sen, U.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012

Title: Cloning, expression, purification, crystallization and preliminary X-ray analysis of a fructokinase from Vibrio cholerae O395
Authors: Paul, R. / Nath, S. / Sen, U.
DepositionNov 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / 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 / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure visualization

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Deposited unit
A: Fructokinase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)35,1993
A: Fructokinase
hetero molecules

A: Fructokinase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)70,3976
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2760 Å2
ΔGint-27 kcal/mol
Surface area24630 Å2
Unit cell
Length a, b, c (Å)117.533, 64.897, 41.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions



#1: Protein Fructokinase /

Mass: 34995.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: cscK, VC0395_0600 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AER7, fructokinase
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / Fructose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
b-D-fructofuranoseCOMMON NAMEGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION

Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION

Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 5% PEG 6000, 0.1M MES, pH 6.0, 7 days / PH range: 6

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 15710 / % possible obs: 94 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.7 / % possible all: 96.6


MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TZ6
Resolution: 2.3→25.667 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 726 5.1 %
Rwork0.1869 --
obs0.1905 14231 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→25.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 13 203 2555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112404
X-RAY DIFFRACTIONf_angle_d1.0943272
X-RAY DIFFRACTIONf_dihedral_angle_d15.907847
X-RAY DIFFRACTIONf_chiral_restr0.069373
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.47750.32361430.23582667X-RAY DIFFRACTION96
2.4775-2.72660.28851410.22172733X-RAY DIFFRACTION98
2.7266-3.12050.27581760.20742706X-RAY DIFFRACTION98
3.1205-3.92930.25751400.17932616X-RAY DIFFRACTION93
3.9293-25.66860.20951260.15582783X-RAY DIFFRACTION93
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)
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 182 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 244 )
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 323 )

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