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- PDB-3w4s: Myo-inositol kinase from Thermococcus kodakarensis -

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Basic information

Entry
Database: PDB / ID: 3w4s
TitleMyo-inositol kinase from Thermococcus kodakarensis
ComponentsCarbohydrate/pyrimidine kinase, PfkB family
KeywordsTRANSFERASE / kinase
Function / homologyRibokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / kinase activity / nucleotide binding / 3-Layer(aba) Sandwich / Alpha Beta / IODIDE ION / Carbohydrate/pyrimidine kinase, PfkB family
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsFujihashi, M. / Miyamoto, Y. / Miki, K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity.
Authors: Sato, T. / Fujihashi, M. / Miyamoto, Y. / Kuwata, K. / Kusaka, E. / Fujita, H. / Miki, K. / Atomi, H.
History
DepositionJan 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate/pyrimidine kinase, PfkB family
B: Carbohydrate/pyrimidine kinase, PfkB family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,49132
Polymers60,6842
Non-polymers3,80730
Water6,557364
1
A: Carbohydrate/pyrimidine kinase, PfkB family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,26124
Polymers30,3421
Non-polymers2,91923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbohydrate/pyrimidine kinase, PfkB family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2308
Polymers30,3421
Non-polymers8887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.306, 78.338, 83.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbohydrate/pyrimidine kinase, PfkB family


Mass: 30341.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2285 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JDA3
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18-23%(w/v) PEG3350, 0.2M NH4I, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.6 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: default / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 50297 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.074 / Net I/σ(I): 38.8
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 13.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.78→41.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.447 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24015 2568 5.1 %RANDOM
Rwork0.19322 ---
obs0.19556 47523 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.78→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 30 364 4635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194561
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9846214
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62623.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55915789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2591530
X-RAY DIFFRACTIONr_chiral_restr0.0860.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213520
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.777→1.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 202 -
Rwork0.217 3380 -
obs--96.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0434-0.06790.05640.6843-0.12130.4348-0.00810.0141-0.0080.0462-0.03370.0038-0.07180.05880.04180.0161-0.0172-0.01320.05930.00260.029315.847176.4536.6806
20.07120.11180.02330.61350.35360.3527-0.0054-0.02350.02340.01790.00260.02750.02980.02860.00280.00340.0068-0.00160.0638-0.01660.049912.895639.1933-18.9701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 273
2X-RAY DIFFRACTION2B1 - 273

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