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- PDB-1v19: 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1v19
Title2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS
Components2-KETO-3-DEOXYGLUCONATE KINASE
KeywordsTRANSFERASE / 2-KETO-3-DEOXYGLUCONATE KINASE / 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
1,4-DIETHYLENE DIOXIDE / 2-dehydro-3-deoxygluconokinase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 12, 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0283
Polymers66,9402
Non-polymers881
Water1,964109
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)201,0859
Polymers200,8216
Non-polymers2643
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
Unit cell
Length a, b, c (Å)84.825, 84.825, 168.494
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.: 2
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-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.61 Å3/Da / Density % sol: 53 % / Description: CRYSTAL IS TWINNED
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.7
Details: MICROBATCH METHOD AT 291 K. 22.8 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 44% MPD, 10% DIOXANE AND 0.1 M HEPES BUFFER PH 7.7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 32439 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 9.1 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 29.6
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / % possible all: 97.1

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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 1RKD

1rkd


Resolution: 2.3→44.62 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 444263.74 / 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 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 1422 4.7 %RANDOM
Rwork0.1529 ---
obs0.1529 30051 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.301 Å2 / ksol: 0.351572 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.377 Å2-5.06 Å20 Å2
2---4.377 Å20 Å2
3---8.753 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 6 109 4709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.691.5
X-RAY DIFFRACTIONc_mcangle_it6.842
X-RAY DIFFRACTIONc_scbond_it7.532
X-RAY DIFFRACTIONc_scangle_it10.642.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 144 4.6 %
Rwork0.2781 2708 -
obs--94.98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3DOX.PARDOX.TOP

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