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- PDB-2dcn: Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolob... -

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Basic information

Entry
Database: PDB / ID: 2dcn
TitleCrystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate (alpha-furanose form)
Componentshypothetical fructokinase
KeywordsTRANSFERASE / 2-keto-3-deoxygluconate kinase / sulfolobus tokodaii / 2-keto-D-gluconate
Function / homology
Function and homology information


2-dehydro-3-deoxygluconokinase / 2-dehydro-3-deoxygluconokinase activity / ATP binding
Similarity search - Function
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 / 6-O-phosphono-beta-D-psicofuranosonic acid / : / 2-dehydro-3-deoxygluconokinase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOkazaki, S. / Onda, H. / Suzuki, A. / Kuramitsu, S. / Masui, R. / Yamane, T.
CitationJournal: To be Published
Title: Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate
Authors: Okazaki, S. / Onda, H. / Suzuki, A. / Kuramitsu, S. / Masui, R. / Yamane, T.
History
DepositionJan 10, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3May 24, 2017Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: hypothetical fructokinase
B: hypothetical fructokinase
C: hypothetical fructokinase
D: hypothetical fructokinase
E: hypothetical fructokinase
F: hypothetical fructokinase
G: hypothetical fructokinase
H: hypothetical fructokinase
I: hypothetical fructokinase
J: hypothetical fructokinase
K: hypothetical fructokinase
L: hypothetical fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)424,23492
Polymers414,28012
Non-polymers9,95480
Water34,7691930
1
A: hypothetical fructokinase
B: hypothetical fructokinase
C: hypothetical fructokinase
D: hypothetical fructokinase
E: hypothetical fructokinase
F: hypothetical fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,09345
Polymers207,1406
Non-polymers4,95339
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27460 Å2
ΔGint-322 kcal/mol
Surface area58030 Å2
MethodPISA, PQS
2
G: hypothetical fructokinase
H: hypothetical fructokinase
I: hypothetical fructokinase
J: hypothetical fructokinase
K: hypothetical fructokinase
L: hypothetical fructokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,14147
Polymers207,1406
Non-polymers5,00241
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27660 Å2
ΔGint-338 kcal/mol
Surface area57850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.638, 150.229, 154.757
Angle α, β, γ (deg.)90, 93.73, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 24 molecules ABCDEFGHIJKL

#1: Protein
hypothetical fructokinase / 2-keto-3-deoxygluconate kinase


Mass: 34523.301 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96XN9, 2-dehydro-3-deoxygluconokinase
#4: Sugar
ChemComp-CKP / 6-O-phosphono-beta-D-psicofuranosonic acid / (2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[(PHOSPHONATOOXY)METHYL]TETRAHYDROFURAN-2-CARBOXYLIC ACID / 2-KETO-6-PHOSPHATE-D-GLUCONIC ACID, ALPHA-FURANOSE FORM / 6-O-phosphono-beta-D-psicosonic acid / 6-O-phosphono-D-psicosonic acid / 6-O-phosphono-psicosonic acid


Type: D-saccharide / Mass: 274.119 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H11O10P

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Non-polymers , 4 types, 1998 molecules

#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1930 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 179988 / Num. obs: 179988 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.089 / Rsym value: 0.064
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.377 / Rsym value: 0.292 / % possible all: 82.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→46.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.247 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS
RfactorNum. reflection% reflectionSelection details
Rfree0.22817 9064 5 %RANDOM
Rwork0.17485 ---
all0.17758 183508 --
obs0.17758 170891 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.797 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28860 0 584 1930 31374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02230395
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.99341218
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11753758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6524.6711291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.313155269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.84615110
X-RAY DIFFRACTIONr_chiral_restr0.0960.24525
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222622
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.215651
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.221072
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.22187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.218
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.2150
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5451.518534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.055229819
X-RAY DIFFRACTIONr_scbond_it1.773312077
X-RAY DIFFRACTIONr_scangle_it2.8574.511399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.246→2.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 560 -
Rwork0.235 10716 -
obs--84.17 %

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