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- PDB-5ygg: Crystal structure of Fructokinase Double-Mutant (T261C-H108C) fro... -

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Basic information

Entry
Database: PDB / ID: 5ygg
TitleCrystal structure of Fructokinase Double-Mutant (T261C-H108C) from Vibrio cholerae O395 in fructose, ADP and potassium ion bound form
ComponentsFructokinase
KeywordsTRANSFERASE / Kinase / Sugar Binding / Double Mutant
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 / beta-D-fructofuranose / : / Fructokinase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.671 Å
AuthorsChatterjee, S. / Paul, R. / Nath, S. / Sen, U.
CitationJournal: Sci Rep / Year: 2018
Title: Large-scale conformational changes and redistribution of surface negative charge upon sugar binding dictate the fidelity of phosphorylation in Vibrio cholerae fructokinase.
Authors: Paul, R. / Chatterjee, S. / Nath, S. / Sen, U.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _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 1.3Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6495
Polymers34,9631
Non-polymers6874
Water6,161342
1
A: Fructokinase
hetero molecules

A: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,29810
Polymers69,9252
Non-polymers1,3738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_567x,-y+1,-z+21
Buried area4320 Å2
ΔGint-39 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.760, 64.330, 116.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-966-

HOH

21A-982-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Fructokinase /


Mass: 34962.555 Da / Num. of mol.: 1 / Mutation: T261C, H108C
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
#3: 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 , 4 types, 345 molecules

#2: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, calcium chloride, ADP, Fructose, Potassium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→33.92 Å / Num. obs: 36538 / % possible obs: 97.5 % / Redundancy: 3.5 % / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EY7

5ey7


Resolution: 1.671→10.06 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.98
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1776 4.86 %0.05
Rwork0.1631 ---
obs0.1647 36538 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.671→10.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 41 342 2723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122438
X-RAY DIFFRACTIONf_angle_d1.1153314
X-RAY DIFFRACTIONf_dihedral_angle_d14.281855
X-RAY DIFFRACTIONf_chiral_restr0.045378
X-RAY DIFFRACTIONf_plane_restr0.006430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6713-1.71650.29021300.26712530X-RAY DIFFRACTION96
1.7165-1.7670.27081570.22392666X-RAY DIFFRACTION100
1.767-1.8240.27031330.20012695X-RAY DIFFRACTION100
1.824-1.88920.23391150.19262691X-RAY DIFFRACTION100
1.8892-1.96480.23081300.18682704X-RAY DIFFRACTION100
1.9648-2.05420.20681320.15942655X-RAY DIFFRACTION100
2.0542-2.16250.16991390.15792681X-RAY DIFFRACTION100
2.1625-2.2980.18821190.15672724X-RAY DIFFRACTION99
2.298-2.47540.19271350.15212706X-RAY DIFFRACTION99
2.4754-2.72440.20891370.15712667X-RAY DIFFRACTION99
2.7244-3.11840.191620.15662651X-RAY DIFFRACTION98
3.1184-3.92790.1681460.13782672X-RAY DIFFRACTION96
3.9279-10.060.15781410.15322720X-RAY DIFFRACTION93
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4662-0.20470.67621.2212-0.06561.1820.1035-0.0462-0.04480.02330.04840.130.0921-0.1749-0.16950.0724-0.00970.0230.08930.04250.0914.948126.0423132.2808
20.9368-0.1498-0.18810.7268-0.2460.86950.04940.07560.0369-0.0388-0.02690.0059-0.02110.011-0.01410.0627-0.0044-0.00590.0540.01130.056514.264123.5305131.2492
31.0804-0.32080.21040.8716-0.50190.50150.05990.0289-0.1792-0.074-0.01410.04090.1155-0.0165-0.03550.10610.0034-0.01570.08850.01050.11613.93419.5872138.099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 323 )

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