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- PDB-7e4l: Conversion of pyrophosphate-dependent myo-inositol-1 kinase into ... -

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Basic information

Entry
Database: PDB / ID: 7e4l
TitleConversion of pyrophosphate-dependent myo-inositol-1 kinase into myo-inositol-3 kinase by N78L/S89L mutation
ComponentsPfkB domain-containing protein
KeywordsTRANSFERASE / pyrophosphate-dependent kinase
Function / homologyPPi-dependent kinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / METHYLENEDIPHOSPHONIC ACID / PfkB domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsTashiro, R. / Miki, K. / Fujihashi, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Altering the Phosphorylation Position of Pyrophosphate-Dependent myo -Inositol-1-Kinase Based on Its Crystal Structure.
Authors: Tashiro, R. / Sato, T. / Atomi, H. / Miki, K. / Fujihashi, M.
History
DepositionFeb 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: PfkB domain-containing protein
B: PfkB domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6606
Polymers64,2602
Non-polymers4014
Water3,477193
1
A: PfkB domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3303
Polymers32,1301
Non-polymers2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area11690 Å2
MethodPISA
2
B: PfkB domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3303
Polymers32,1301
Non-polymers2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-5 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.205, 46.398, 66.544
Angle α, β, γ (deg.)83.53, 80.43, 68.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PfkB domain-containing protein / pyrophosphate-dependent myo-inositol-1 kinase


Mass: 32129.789 Da / Num. of mol.: 2 / Mutation: N78L/S89L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: Tmari_0412 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: R4NYE9
#2: Chemical ChemComp-MDN / METHYLENEDIPHOSPHONIC ACID


Mass: 176.002 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH6O6P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 26% (w/v) poly(ethylene glycol) 4000, 2mM ammonium sulfate, 100mM sodium acetate buffer (pH 5.4)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 43707 / % possible obs: 62.5 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rrim(I) all: 0.051 / Net I/σ(I): 19.8
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.58 % / Mean I/σ(I) obs: 9.1 / Num. unique obs: 4684 / CC1/2: 0.985 / Rrim(I) all: 0.134 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ysp

5ysp


Resolution: 1.6→42.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21555 2173 5 %RANDOM
Rwork0.19179 ---
obs0.19301 41534 65.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20.21 Å20.15 Å2
2---0.33 Å20.32 Å2
3---0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.6→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 20 193 4479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134399
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174176
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.6425958
X-RAY DIFFRACTIONr_angle_other_deg2.3071.5789582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02420.952210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65815728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.991531
X-RAY DIFFRACTIONr_chiral_restr0.0570.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024939
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021027
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_it0.8941.6072233
X-RAY DIFFRACTIONr_mcbond_other0.8931.6062232
X-RAY DIFFRACTIONr_mcangle_it1.5132.4072790
X-RAY DIFFRACTIONr_mcangle_other1.5132.4072791
X-RAY DIFFRACTIONr_scbond_it1.0471.7232166
X-RAY DIFFRACTIONr_scbond_other1.0481.7242164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6892.5373168
X-RAY DIFFRACTIONr_long_range_B_refined3.23318.5684755
X-RAY DIFFRACTIONr_long_range_B_other3.21818.5274744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 218 -
Rwork0.218 4459 -
obs--94.47 %

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