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- PDB-5f0z: Crystal structure of Fructokinase from Vibrio cholerae O395 in fr... -

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Basic information

Entry
Database: PDB / ID: 5f0z
TitleCrystal structure of Fructokinase from Vibrio cholerae O395 in fructose, ADP and calcium ion bound form
ComponentsFructokinase
KeywordsTRANSFERASE / kinase / fructose / ADP
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
ADENOSINE-5'-DIPHOSPHATE / beta-D-fructofuranose / Fructokinase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPaul, R. / Nath, S. / Sen, U.
Funding support India, 1items
OrganizationGrant numberCountry
Department od Atomic Energy, Govt. of India 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: 2015
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 28, 2015Deposition site: PDBJ / 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

Downloads & links

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Assembly

Deposited unit
A: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6665
Polymers34,9961
Non-polymers6704
Water6,305350
1
A: Fructokinase
hetero molecules

A: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,33210
Polymers69,9912
Non-polymers1,3418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4580 Å2
ΔGint-66 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.884, 64.272, 41.731
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-787-

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 , 4 types, 353 molecules

#3: 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-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.1 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, 3-4 days / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 30437 / % possible obs: 95.1 % / Redundancy: 3.15 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 6.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.3 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TZ6

1tz6


Resolution: 1.75→35 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1865 1497 5.08 %Random selection
Rwork0.1477 ---
obs0.1497 29487 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 41 350 2730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122452
X-RAY DIFFRACTIONf_angle_d1.3053357
X-RAY DIFFRACTIONf_dihedral_angle_d14.958865
X-RAY DIFFRACTIONf_chiral_restr0.077379
X-RAY DIFFRACTIONf_plane_restr0.007433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.27461360.23722513X-RAY DIFFRACTION100
1.8065-1.8710.23021440.19052511X-RAY DIFFRACTION100
1.871-1.9460.22191430.1782528X-RAY DIFFRACTION100
1.946-2.03450.23211390.16722501X-RAY DIFFRACTION100
2.0345-2.14180.1871290.14752554X-RAY DIFFRACTION100
2.1418-2.27590.17591280.13862536X-RAY DIFFRACTION100
2.2759-2.45160.17341470.13612566X-RAY DIFFRACTION100
2.4516-2.69820.16761410.13692540X-RAY DIFFRACTION100
2.6982-3.08850.19661430.1462557X-RAY DIFFRACTION99
3.0885-3.89040.18581230.12472583X-RAY DIFFRACTION98
3.8904-35.00750.1511240.14842601X-RAY DIFFRACTION94
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)
12.76650.01730.69232.27050.06722.6537-0.08820.0853-0.0566-0.20010.0934-0.10860.07290.03230.09040.0681-0.01110.04960.0108-0.0060.01414.57577.9612-14.795
21.55740.6864-0.58321.3302-0.11921.6101-0.08030.043-0.1629-0.09630.0188-0.04440.1173-0.01920.04890.0862-0.02190.00770.0488-0.01060.06412.19474.4151-12.4818
31.52720.7454-0.27141.322-0.26180.91730.0304-0.06650.12540.0747-0.01690.0414-0.0409-0.025-0.00210.0614-0.0102-0.00610.0518-0.01330.061214.156117.7315-1.0368
41.14640.53650.45961.66940.83961.4351-0.13180.1310.1491-0.15460.0884-0.0216-0.17950.08820.0430.1011-0.0395-0.01360.09330.02340.078919.577923.8199-17.6317
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 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 222 )
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 323 )

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