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- PDB-1v1s: 2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS (CRYSTAL... -

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Basic information

Entry
Database: PDB / ID: 1v1s
Title2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS (CRYSTAL FORM 2)
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
2-dehydro-3-deoxygluconokinase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 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
E: 2-KETO-3-DEOXYGLUCONATE KINASE
F: 2-KETO-3-DEOXYGLUCONATE KINASE


Theoretical massNumber of molelcules
Total (without water)200,8216
Polymers200,8216
Non-polymers00
Water0
1
A: 2-KETO-3-DEOXYGLUCONATE KINASE
B: 2-KETO-3-DEOXYGLUCONATE KINASE

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

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


Theoretical massNumber of molelcules
Total (without water)200,8216
Polymers200,8216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
2
C: 2-KETO-3-DEOXYGLUCONATE KINASE
D: 2-KETO-3-DEOXYGLUCONATE KINASE

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

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


Theoretical massNumber of molelcules
Total (without water)200,8216
Polymers200,8216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
3
E: 2-KETO-3-DEOXYGLUCONATE KINASE
F: 2-KETO-3-DEOXYGLUCONATE KINASE

E: 2-KETO-3-DEOXYGLUCONATE KINASE
F: 2-KETO-3-DEOXYGLUCONATE KINASE

E: 2-KETO-3-DEOXYGLUCONATE KINASE
F: 2-KETO-3-DEOXYGLUCONATE KINASE


Theoretical massNumber of molelcules
Total (without water)200,8216
Polymers200,8216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation2_545-y,x-y-1,z1
MethodPQS
Unit cell
Length a, b, c (Å)145.831, 145.831, 74.633
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 33470.184 Da / Num. of mol.: 6
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

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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: 2.28 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: VAPOUR-DIFFUSION SITTING DROP, AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 28% V/V MPD, 10 MM CALCIUM CHLORIDE AND 0.1 M TRISODIUM CITRATE BUFFER, PH 5.6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 27126 / % possible obs: 92.9 % / Observed criterion σ(I): -1 / Redundancy: 3.43 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.46
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2 / % possible all: 82

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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: 3.2→29.4 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 118387.2 / 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
Rfree0.2778 1205 4.1 %RANDOM
Rwork0.2391 ---
obs0.2391 27163 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.7918 Å2 / ksol: 0.235014 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.584 Å2-1.876 Å20 Å2
2--4.584 Å20 Å2
3----9.169 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13782 0 0 0 13782
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
Refine LS restraints NCSNCS model details: RESTRAIN / Rms dev position: 0 Å / Weight position: 300
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3423 114 3.9 %
Rwork0.2953 1930 -
obs--69.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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