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- PDB-6e7f: Crystal Structure of Human Inositol Polyphosphate Multikinase (IP... -

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Basic information

Entry
Database: PDB / ID: 6e7f
TitleCrystal Structure of Human Inositol Polyphosphate Multikinase (IPMK) Catalytic Core Domain
ComponentsInositol polyphosphate multikinase
KeywordsTRANSFERASE / Kinase / Inositol phosphate / IPMK
Function / homology
Function and homology information


Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol tetrakisphosphate 5-kinase activity / myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol tetrakisphosphate 3-kinase activity / flavonoid binding / inositol tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate kinase activity ...Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol tetrakisphosphate 5-kinase activity / myo-inositol-1,2,3,4,6-heptakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol tetrakisphosphate 3-kinase activity / flavonoid binding / inositol tetrakisphosphate 6-kinase activity / inositol tetrakisphosphate 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 / phosphorylation / 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: 2.5 Å
AuthorsBlind, R. / Seacrist, C.
Funding support United States, 2items
OrganizationGrant numberCountry
American Cancer SocietyRSG-17-063-01 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K01 CA172957 United States
CitationJournal: Sci Rep / Year: 2018
Title: Crystallographic and kinetic analyses of human IPMK reveal disordered domains modulate ATP binding and kinase activity.
Authors: Seacrist, C.D. / Blind, R.D.
History
DepositionJul 26, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionNov 7, 2018ID: 6C8A
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0205
Polymers63,7322
Non-polymers2883
Water1,29772
1
A: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9622
Polymers31,8661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0583
Polymers31,8661
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.660, 109.360, 73.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

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


Mass: 31866.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IMPK / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8NFU5, inositol-polyphosphate multikinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.05 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, pH 3.5, 0.8 M (NH4)2 SO4, 1 mM AMPPNP, 1 mM MnCl2, 0.73 mM Inositol (1,3,4,6)tetra phosphate (IP4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→43.89 Å / Num. obs: 27377 / % possible obs: 99.96 % / Redundancy: 6.4 % / Biso Wilson estimate: 53.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08007 / Rpim(I) all: 0.03411 / Rrim(I) all: 0.08719 / Net I/σ(I): 18.76
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.3281 / Mean I/σ(I) obs: 4.25 / Num. unique obs: 2694 / CC1/2: 0.982 / Rpim(I) all: 0.1499 / Rrim(I) all: 0.362 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
BALBESphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IF8

2if8


Resolution: 2.5→43.89 Å / SU ML: 0.4192 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 29.8575
RfactorNum. reflection% reflection
Rfree0.2803 1364 4.98 %
Rwork0.2265 --
obs0.2292 27377 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 15 72 3923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983951
X-RAY DIFFRACTIONf_angle_d1.15385341
X-RAY DIFFRACTIONf_chiral_restr0.059561
X-RAY DIFFRACTIONf_plane_restr0.0062680
X-RAY DIFFRACTIONf_dihedral_angle_d5.37382341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.36231310.30162563X-RAY DIFFRACTION100
2.59-2.690.34611350.29552552X-RAY DIFFRACTION100
2.69-2.820.40161400.27542558X-RAY DIFFRACTION100
2.82-2.960.34021430.25532553X-RAY DIFFRACTION100
2.96-3.150.31931340.23632561X-RAY DIFFRACTION100
3.15-3.390.30671370.24132603X-RAY DIFFRACTION100
3.39-3.730.25471360.22432587X-RAY DIFFRACTION100
3.73-4.270.25291250.20182629X-RAY DIFFRACTION100
4.27-5.380.2571300.19362646X-RAY DIFFRACTION100
5.38-43.90.25351530.22882761X-RAY DIFFRACTION99.9

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