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- PDB-1ko5: Crystal structure of gluconate kinase -

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Basic information

Entry
Database: PDB / ID: 1ko5
TitleCrystal structure of gluconate kinase
ComponentsGluconate kinase
KeywordsTRANSFERASE / alfa/beta
Function / homology
Function and homology information


gluconokinase / gluconokinase activity / D-gluconate catabolic process / protein homodimerization activity / ATP binding
Similarity search - Function
Carbohydrate kinase, thermoresistant glucokinase / Shikimate kinase/gluconokinase / Shikimate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Thermoresistant gluconokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKraft, L. / Sprenger, G.A. / Lindqvist, Y.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography.
Authors: Kraft, L. / Sprenger, G.A. / Lindqvist, Y.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gluconate kinase
B: Gluconate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2086
Polymers39,1452
Non-polymers1,0634
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.274, 89.206, 51.479
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer

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Components

#1: Protein Gluconate kinase / Thermoresistant gluconokinase


Mass: 19572.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gntk / Plasmid: pJF119EH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P46859, gluconokinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
33 mM1dropMgCl2
41 mMdithiothreitol1drop
517-20 %(w/v)PEG60001reservoir
61.4-1.7 M1reservoirLiCl
70.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.845 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.845 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 17024 / Num. obs: 17024 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.049 / Net I/σ(I): 27.8
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.254 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 50986 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.254

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.319 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27657 789 4.8 %RANDOM
Rwork0.21356 ---
all0.21665 15607 --
obs0.21665 15607 95.51 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.153 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å21.13 Å2
2--0.26 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.28→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 64 94 2860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212822
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9773826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7353342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59515504
X-RAY DIFFRACTIONr_chiral_restr0.0980.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022104
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.31319
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.354
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.59
X-RAY DIFFRACTIONr_mcbond_it0.6861.51710
X-RAY DIFFRACTIONr_mcangle_it1.29522750
X-RAY DIFFRACTIONr_scbond_it1.93331112
X-RAY DIFFRACTIONr_scangle_it3.2414.51076
LS refinement shellResolution: 2.284→2.343 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 47
Rwork0.248 1025
Refinement
*PLUS
Rfactor obs: 0.214 / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.214 / Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.54
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / Rfactor Rwork: 0.248

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