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- PDB-4u7x: Crystal structure of Fructokinase from Brucella abortus 2308 -

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Basic information

Entry
Database: PDB / ID: 4u7x
TitleCrystal structure of Fructokinase from Brucella abortus 2308
ComponentsRibokinase:Carbohydrate kinase, PfkB
KeywordsTRANSFERASE / kinase / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


fructokinase / fructokinase activity
Similarity search - Function
Ribokinase/fructokinase / 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
Ribokinase:Carbohydrate kinase, PfkB
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of Fructokinase from Brucella abortus 2308
Authors: Horanyi, P.S. / Fox III, D. / Abendroth, J. / Lorimer, D. / Edwards, T.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribokinase:Carbohydrate kinase, PfkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1875
Polymers34,0951
Non-polymers924
Water1,45981
1
A: Ribokinase:Carbohydrate kinase, PfkB
hetero molecules

A: Ribokinase:Carbohydrate kinase, PfkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,37410
Polymers68,1902
Non-polymers1848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area3460 Å2
ΔGint-118 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.900, 103.900, 61.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ribokinase:Carbohydrate kinase, PfkB / Fructokinase


Mass: 34094.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: cscK, BAB1_0112 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YNY7, fructokinase
#2: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 16, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 20243 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.91 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.055 / Χ2: 1.005 / Net I/σ(I): 33.45 / Num. measured all: 331382
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.150.9220.4944.6814498147914790.52100
2.15-2.210.9540.385.9713737141614160.4100
2.21-2.280.9660.3167.413724139913990.333100
2.28-2.350.9830.2668.6213054133913390.28100
2.35-2.420.9850.37611.2825118131013100.385100
2.42-2.510.990.30413.7224863127312730.312100
2.51-2.60.9920.2416.6223948123912390.247100
2.6-2.710.9960.16822.3322912118211820.173100
2.71-2.830.9980.13127.8422241114711470.134100
2.83-2.970.9980.10133.3721089109410940.104100
2.97-3.130.9990.07641.8320162104210420.078100
3.13-3.320.9990.0649.85189559899880.06199.9
3.32-3.550.9990.04561.42177629329320.046100
3.55-3.8310.0468.91166748848840.041100
3.83-4.210.03575.79150078068050.03699.9
4.2-4.710.03283.01138657517500.03399.9
4.7-5.4210.03281.08119826576570.033100
5.42-6.6410.03279.34102725735730.033100
6.64-9.3910.02684.3878404604590.02799.8
9.3910.0237436792882750.02495.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.614

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
MOLREPphasing
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.465 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1018 5.04 %Random
Rwork0.2152 19177 --
obs0.217 20195 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.74 Å2 / Biso mean: 50.5043 Å2 / Biso min: 22.88 Å2
Refinement stepCycle: final / Resolution: 2.1→46.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 4 81 2432
Biso mean--55.92 47.62 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072420
X-RAY DIFFRACTIONf_angle_d0.9963299
X-RAY DIFFRACTIONf_chiral_restr0.039383
X-RAY DIFFRACTIONf_plane_restr0.005432
X-RAY DIFFRACTIONf_dihedral_angle_d12.801857
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.21080.34631360.303326972833100
2.2108-2.34930.3641500.298126642814100
2.3493-2.53060.35541450.302527112856100
2.5306-2.78530.31821360.27427082844100
2.7853-3.18820.29461590.256227312890100
3.1882-4.01650.23711470.195327622909100
4.0165-46.47680.17991450.16042904304999

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