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- PDB-2var: Crystal structure of Sulfolobus solfataricus 2-keto-3-deoxyglucon... -

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Basic information

Entry
Database: PDB / ID: 2var
TitleCrystal structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase complexed with 2-keto-3-deoxygluconate
ComponentsFRUCTOKINASE
KeywordsTRANSFERASE / KINASE / SULFOLOBUS SOLFATARICUS / PFKB FAMILY CARBOHYDRATE KINASE / 2- KETO-3-DEOXYGLUCONATE KINASEKINASE / 2- KETO-3-DEOXYGLUCONATE KINASE
Function / homology
Function and homology information


2-dehydro-3-deoxyglucono/galactono-kinase / 2-dehydro-3-deoxygalactonokinase activity / 2-dehydro-3-deoxygluconokinase activity / phosphorylation / nucleotide binding / 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 MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 3-deoxy-alpha-D-erythro-hex-2-ulofuranosonic acid / 2-KETO-3-DEOXYGLUCONATE / 2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPotter, J.A. / Theodossis, A. / Kerou, M. / Lamble, H.J. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: The Structure of Sulfolobus Solfataricus 2-Keto-3-Deoxygluconate Kinase.
Authors: Potter, J.A. / Kerou, M. / Lamble, H.J. / Bull, S.D. / Hough, D.W. / Danson, M.J. / Taylor, G.L.
History
DepositionSep 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_database_status / 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.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 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

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Assembly

Deposited unit
A: FRUCTOKINASE
B: FRUCTOKINASE
C: FRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,38515
Polymers104,7563
Non-polymers3,62912
Water8,233457
1
A: FRUCTOKINASE
B: FRUCTOKINASE
C: FRUCTOKINASE
hetero molecules

A: FRUCTOKINASE
B: FRUCTOKINASE
C: FRUCTOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,77030
Polymers209,5126
Non-polymers7,25824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area30640 Å2
ΔGint-111.6 kcal/mol
Surface area58400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.553, 104.553, 420.782
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.491, 0.364, 0.792), (0.312, -0.775, 0.55), (0.814, 0.517, 0.267)-74.49827, 15.89416, 40.4232
2given(-0.508, -0.359, -0.783), (0.319, 0.766, -0.558), (0.8, -0.534, -0.275)-74.90893, 16.28102, 39.89122

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein FRUCTOKINASE / 2-KETO-3-DEOXYGLUCONATE KINASE


Mass: 34918.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97U29, fructokinase
#3: Sugar ChemComp-KDF / 3-deoxy-alpha-D-erythro-hex-2-ulofuranosonic acid / 2-keto-3-deoxygluconate / 3-deoxy-alpha-D-erythro-hex-2-ulosonic acid / 3-deoxy-D-erythro-hex-2-ulosonic acid / 3-deoxy-erythro-hex-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 178.140 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O6

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Non-polymers , 4 types, 466 molecules

#2: Chemical ChemComp-KDG / 2-KETO-3-DEOXYGLUCONATE


Mass: 178.140 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O6
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 57.84 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→90.5 Å / Num. obs: 80339 / % possible obs: 99.8 % / Observed criterion σ(I): 4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / % possible all: 99.5

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→61.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.825 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4008 5 %RANDOM
Rwork0.181 ---
obs0.183 76307 99.6 %-
Displacement parametersBiso mean: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→61.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 234 457 8026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.72.01210548
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87924.481337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.034151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0191542
X-RAY DIFFRACTIONr_chiral_restr0.1150.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025731
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23777
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.25309
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2478
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2127
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.54824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42527549
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42533383
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5084.52994
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 265
Rwork0.221 5491

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