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- PDB-5ey7: Crystal structure of Fructokinase from Vibrio cholerae O395 in ap... -

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Basic information

Entry
Database: PDB / ID: 5ey7
TitleCrystal structure of Fructokinase from Vibrio cholerae O395 in apo form
ComponentsFructokinase
KeywordsTRANSFERASE / kinase / fructose phosphorylation / apo
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
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.461 Å
AuthorsPaul, R. / Nath, S. / Sen, U.
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 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / pdbx_related_exp_data_set / Item: _citation.journal_id_CSD
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructokinase
B: Fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0143
Polymers69,9912
Non-polymers231
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-24 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.116, 99.858, 61.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Fructokinase /


Mass: 34995.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Vibrio cholerae O395 fructokinase in apo form
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 5% PEG 6000, 0.1M MES, pH 6.0 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 23435 / % possible obs: 94.3 % / Redundancy: 2.73 % / Rmerge(I) obs: 0.056 / Net I/av σ(I): 1.9 / Net I/σ(I): 6.7
Reflection shellResolution: 2.46→2.64 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.9 / % possible all: 95.01

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
AUTOMARdata reduction
AUTOMARdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TZ6

1tz6


Resolution: 2.461→29.409 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1172 5.01 %
Rwork0.2155 --
obs0.2169 23398 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.461→29.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4543 0 1 83 4627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034640
X-RAY DIFFRACTIONf_angle_d0.7376313
X-RAY DIFFRACTIONf_dihedral_angle_d15.9021647
X-RAY DIFFRACTIONf_chiral_restr0.029716
X-RAY DIFFRACTIONf_plane_restr0.003833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4607-2.57260.40331380.33592618X-RAY DIFFRACTION91
2.5726-2.70820.2871410.28982817X-RAY DIFFRACTION98
2.7082-2.87770.30781550.27672822X-RAY DIFFRACTION98
2.8777-3.09970.32131500.28562826X-RAY DIFFRACTION98
3.0997-3.41120.2681480.24262819X-RAY DIFFRACTION97
3.4112-3.90380.25171480.20882801X-RAY DIFFRACTION96
3.9038-4.91470.19911420.16832780X-RAY DIFFRACTION94
4.9147-29.41120.17761500.172743X-RAY DIFFRACTION89
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)
11.7308-0.6474-0.19531.7732-1.51248.2484-0.2935-0.9432-0.21240.27610.0685-0.08080.59770.54080.56090.47480.00860.0140.9919-0.0990.4162.54127.4195-28.2499
22.4979-0.55370.88922.1967-0.03483.6898-0.1429-0.69780.8040.26320.1344-0.4239-0.55270.4129-0.09460.4957-0.0875-0.00090.8207-0.24380.51163.490434.9097-34.414
33.7809-2.02650.06351.36480.78684.1203-0.2529-0.917-0.13730.42060.25490.17910.1021-0.1579-0.06150.4096-0.03570.01410.6104-0.05810.347-6.401327.5232-34.9872
44.3715-0.3989-0.94392.74591.59513.4129-0.0056-0.3143-0.42450.392-0.16690.17440.1207-0.14610.17440.3998-0.0433-0.00620.5159-0.00630.3904-10.657524.6095-44.4583
53.1426-0.2286-1.18124.03660.26462.1546-0.0561-0.3911-1.67540.1001-0.02510.64270.2071-0.55070.04790.4321-0.02510.03350.65140.11170.9139-7.69919.1752-44.7254
65.4564-1.1066-0.39886.3351.01733.92090.3696-0.5875-1.47920.8716-0.34130.29690.58030.261-0.09450.6615-0.05140.03480.59010.14591.01834.00877.7305-39.0019
73.98530.3527-0.84131.99320.46912.8992-0.0929-0.4878-0.66670.19450.005-0.19460.1015-0.03290.14140.34160.01730.0120.6570.02240.489810.783215.7872-40.2128
88.2279-1.155-2.81562.50121.10143.6521-0.1166-0.37920.0352-0.15640.0557-0.1455-0.04221.09580.16420.4063-0.028-0.0170.7716-0.01170.3672-10.186532.3114-6.8336
92.5655-0.57890.67161.6530.8183.0766-0.16110.23390.1763-0.16420.1483-0.0564-0.00060.4740.02490.3584-0.04890.01460.4871-0.02320.339-19.584333.4057-8.6294
101.65460.18891.26752.96340.50275.0921-0.25540.01821.11820.1539-0.0171-0.4064-1.51510.25070.35560.8315-0.0497-0.1610.5862-0.0690.8955-22.170752.6338-0.826
111.46930.32631.48712.4589-0.50212.40630.0877-0.45960.52260.1639-0.11550.087-0.42280.0168-0.00460.6059-0.031-0.07060.5362-0.14650.5251-18.388342.265510.6794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 196 )
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 239 )
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 263 )
7X-RAY DIFFRACTION7chain 'A' and (resid 264 through 323 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 45 )
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 164 )
10X-RAY DIFFRACTION10chain 'B' and (resid 165 through 264 )
11X-RAY DIFFRACTION11chain 'B' and (resid 265 through 307 )

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