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- PDB-5w2g: Crystal structure of the core catalytic domain of human inositol ... -

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Basic information

Entry
Database: PDB / ID: 5w2g
TitleCrystal structure of the core catalytic domain of human inositol phosphate multikinase
ComponentsInositol polyphosphate multikinase,Inositol polyphosphate multikinase
KeywordsTRANSFERASE / kinase / inositol / inositol polyphosphate / phosphatidylinositol / specificity
Function / homology
Function and homology information


inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity ...inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol trisphosphate metabolic process / inositol phosphate metabolic process / inositol phosphate biosynthetic process / phosphatidylinositol metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / necroptotic process / ciliary basal body / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
Inositol polyphosphate multikinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, H. / Shears, S.B.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural features of human inositol phosphate multikinase rationalize its inositol phosphate kinase and phosphoinositide 3-kinase activities.
Authors: Wang, H. / Shears, S.B.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _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: Inositol polyphosphate multikinase,Inositol polyphosphate multikinase


Theoretical massNumber of molelcules
Total (without water)29,4271
Polymers29,4271
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.466, 78.466, 85.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

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Components

#1: Protein Inositol polyphosphate multikinase,Inositol polyphosphate multikinase / Inositol 1 / 3 / 4 / 6-tetrakisphosphate 5-kinase


Mass: 29427.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IMPK / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NFU5, inositol-polyphosphate multikinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 25507 / % possible obs: 99.4 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 15.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2if8

2if8


Resolution: 1.8→46.57 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.362 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21506 1268 5.1 %RANDOM
Rwork0.17066 ---
obs0.17287 23558 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 0 154 2060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192102
X-RAY DIFFRACTIONr_bond_other_d0.0020.021899
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9652869
X-RAY DIFFRACTIONr_angle_other_deg0.934440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05324.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1515366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8011510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02446
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_it1.6382.1461019
X-RAY DIFFRACTIONr_mcbond_other1.642.1451018
X-RAY DIFFRACTIONr_mcangle_it2.2763.2041300
X-RAY DIFFRACTIONr_mcangle_other2.2823.2051301
X-RAY DIFFRACTIONr_scbond_it2.0472.4521083
X-RAY DIFFRACTIONr_scbond_other2.0522.4491080
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6413.581568
X-RAY DIFFRACTIONr_long_range_B_refined3.56126.1582441
X-RAY DIFFRACTIONr_long_range_B_other3.3525.8262411
X-RAY DIFFRACTIONr_rigid_bond_restr1.64934000
X-RAY DIFFRACTIONr_sphericity_free33.75584
X-RAY DIFFRACTIONr_sphericity_bonded17.65954003
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 73 -
Rwork0.246 1457 -
obs--82.84 %
Refinement TLS params.Method: refined / Origin x: 3.2945 Å / Origin y: 17.8706 Å / Origin z: 25.7565 Å
111213212223313233
T0.0065 Å20.0046 Å2-0 Å2-0.0294 Å20.0143 Å2--0.0087 Å2
L0.1453 °2-0.0498 °2-0.0462 °2-0.0389 °2-0.0188 °2--0.094 °2
S-0.0064 Å °0.0014 Å °0.0006 Å °0.008 Å °0.0111 Å °0.0072 Å °-0.0021 Å °0.0029 Å °-0.0046 Å °

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