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

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Basic information

Entry
Database: PDB / ID: 5eyn
TitleCrystal structure of Fructokinase from Vibrio cholerae O395 in fructose, ADP, Beryllium trifluoride and calcium ion bound form
ComponentsFructokinase
KeywordsTRANSFERASE / kinase / fructose
Function / homology
Function and homology information


fructokinase / fructokinase activity / fructose metabolic process / 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / beta-D-fructofuranose / Fructokinase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.289 Å
AuthorsPaul, R. / Nath, S. / Sen, U.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Atomic Energy India
Citation
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.
History
DepositionNov 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7326
Polymers34,9961
Non-polymers7365
Water6,828379
1
A: Fructokinase
hetero molecules

A: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,46412
Polymers69,9912
Non-polymers1,47310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5280 Å2
ΔGint-67 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.300, 107.218, 41.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-785-

HOH

21A-817-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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 / beta-D-fructose / D-fructose / fructose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 383 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% PEG 6000, 0.1M MES, pH 6.0 as precipitant and VcFK (complex with 5 mM ADP + 5 mM Fructose ) + 5 mM BeF3 (soaked)
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.289→32.15 Å / Num. obs: 71986 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 7.5
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.35 / % possible all: 81.1

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tz6

1tz6


Resolution: 1.289→32.15 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1689 3614 5.02 %
Rwork0.1411 --
obs0.1425 71921 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.289→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 45 379 2749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192433
X-RAY DIFFRACTIONf_angle_d1.3743336
X-RAY DIFFRACTIONf_dihedral_angle_d14.012852
X-RAY DIFFRACTIONf_chiral_restr0.069375
X-RAY DIFFRACTIONf_plane_restr0.007427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2894-1.30640.30691220.29762466X-RAY DIFFRACTION93
1.3064-1.32430.29381240.25752612X-RAY DIFFRACTION100
1.3243-1.34320.28811530.23062687X-RAY DIFFRACTION100
1.3432-1.36320.23481380.19812615X-RAY DIFFRACTION100
1.3632-1.38450.20881450.16672642X-RAY DIFFRACTION100
1.3845-1.40720.21321210.16042644X-RAY DIFFRACTION100
1.4072-1.43150.19651550.15382655X-RAY DIFFRACTION100
1.4315-1.45750.21651430.16092627X-RAY DIFFRACTION100
1.4575-1.48560.20451470.16842659X-RAY DIFFRACTION100
1.4856-1.51590.1991550.1482601X-RAY DIFFRACTION100
1.5159-1.54890.20111420.13172681X-RAY DIFFRACTION100
1.5489-1.58490.18651290.1252653X-RAY DIFFRACTION100
1.5849-1.62450.16491490.11652657X-RAY DIFFRACTION100
1.6245-1.66840.16931230.1152689X-RAY DIFFRACTION100
1.6684-1.71750.17531350.12062636X-RAY DIFFRACTION100
1.7175-1.7730.16851460.12412628X-RAY DIFFRACTION99
1.773-1.83630.14251500.12242653X-RAY DIFFRACTION99
1.8363-1.90990.16761400.11842661X-RAY DIFFRACTION99
1.9099-1.99680.15531220.11732658X-RAY DIFFRACTION99
1.9968-2.1020.14861420.1192658X-RAY DIFFRACTION99
2.102-2.23370.15961620.1172619X-RAY DIFFRACTION98
2.2337-2.40610.14621200.13042632X-RAY DIFFRACTION97
2.4061-2.64810.15141380.13032593X-RAY DIFFRACTION96
2.6481-3.03110.15031370.14412581X-RAY DIFFRACTION94
3.0311-3.81780.17791420.13872553X-RAY DIFFRACTION92
3.8178-32.160.16091340.16892547X-RAY DIFFRACTION88

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