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- PDB-1v1b: 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOU... -

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Basic information

Entry
Database: PDB / ID: 1v1b
Title2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP
Components2-KETO-3-DEOXYGLUCONATE KINASE
KeywordsTRANSFERASE / 2-KETO-3-DEOXYGLUCONATE KINASE / ATP / THERMUS THERMOPHILUS / STRUCTURAL GENOMICS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


2-dehydro-3-deoxygluconokinase / 2-dehydro-3-deoxygluconokinase activity / phosphorylation / nucleotide binding / ATP binding
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
ADENOSINE-5'-TRIPHOSPHATE / 2-dehydro-3-deoxygluconokinase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTahirov, T.H. / Inagaki, E.
Citation
Journal: J. Mol. Biol. / Year: 2004
Title: Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.
Authors: Ohshima, N. / Inagaki, E. / Yasuike, K. / Takio, K. / Tahirov, T.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and Preliminary Crystallographic Analysis of 2-Keto-3-Deoxygluconate Kinase from Thermus Thermophilus
Authors: Inagaki, E. / Ukita, Y. / Kumei, M. / Kajihara, Y. / Tahirov, T.H.
History
DepositionApr 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
C: 2-KETO-3-DEOXYGLUCONATE KINASE
D: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9098
Polymers133,8814
Non-polymers2,0294
Water1,67593
1
A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules

A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules

A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,86412
Polymers200,8216
Non-polymers3,0436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
2
C: 2-KETO-3-DEOXYGLUCONATE KINASE
D: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules

C: 2-KETO-3-DEOXYGLUCONATE KINASE
D: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules

C: 2-KETO-3-DEOXYGLUCONATE KINASE
D: 2-KETO-3-DEOXYGLUCONATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,86412
Polymers200,8216
Non-polymers3,0436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.721, 84.721, 321.613
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 33470.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53W83*PLUS
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.54 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: VAPOUR-DIFFUSION SITTING DROP, AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM ATP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH ...Details: VAPOUR-DIFFUSION SITTING DROP, AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM ATP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH 8.5. BEFORE THE DATA COLLECTION THE CRYSTAL WAS SOAKED IN SOLUTION CONTAINING 0.35 M MAGNESIUM CHLORIDE INSTEAD OF AMMONIUM SULFATE. THE CRYOPROTECTANT CONTAINED 33% OF ETHYLENE GLYCOL IN ADDITION TO MAGNESIUM CHLORIDE, BUFFER AND ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU IMAGE PLATE R-AXISV / Detector: IMAGE PLATE / Date: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36923 / % possible obs: 91.7 % / Observed criterion σ(I): -0.4 / Redundancy: 2.41 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.93
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 1.78 / % possible all: 87.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V19

1v19


Resolution: 2.6→29.46 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 438892.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CRYSTAL IS WITH HEMIHEDRAL TWINNING, TWINNING OPERATOR IS "H, -H-K, -L", TWINNING FRACTION IS 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 1628 4.1 %RANDOM
Rwork0.1779 ---
obs0.1779 34007 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3762 Å2 / ksol: 0.346608 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.374 Å2-3.61 Å20 Å2
2---0.374 Å20 Å2
3---0.747 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9156 0 124 93 9373
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.621.5
X-RAY DIFFRACTIONc_mcangle_it5.782
X-RAY DIFFRACTIONc_scbond_it5.032
X-RAY DIFFRACTIONc_scangle_it7.232.5
Refine LS restraints NCSRms dev position: 300 Å
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.372 160 4.02 %
Rwork0.2668 2822 -
obs--74.89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ATP.PARATP.TOP

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