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- PDB-5mwm: INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN... -

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Basic information

Entry
Database: PDB / ID: 5mwm
TitleINOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH IP6
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / protein structure / mammal IPK / inositol kinases
Function / homology
Function and homology information


Synthesis of IPs in the nucleus / Synthesis of pyrophosphates in the cytosol / inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / inositol phosphate biosynthetic process / phosphorylation / ATP binding / nucleus / cytoplasm
Similarity search - Function
Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase, N-terminal lobe / Inositol-pentakisphosphate 2-kinase
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFranco-Echevarria, E. / Sanz-Aparicio, J. / Gonzalez, B.
Funding support Spain, 1items
OrganizationGrant numberCountry
CSICBFU2014-53762-P Spain
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The crystal structure of mammalian inositol 1,3,4,5,6-pentakisphosphate 2-kinase reveals a new zinc-binding site and key features for protein function.
Authors: Franco-Echevarria, E. / Sanz-Aparicio, J. / Brearley, C.A. / Gonzalez-Rubio, J.M. / Gonzalez, B.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Oct 7, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5713
Polymers53,8461
Non-polymers7252
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.550, 71.637, 61.822
Angle α, β, γ (deg.)90.00, 111.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Inositol-pentakisphosphate 2-kinase / / Inositol-1 / 3 / 4 / 5 / 6-pentakisphosphate 2-kinase / Ins(1 / 6)P5 2-kinase / InsP5 2-kinase


Mass: 53846.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ippk / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star
References: UniProt: Q6P1C1, inositol-pentakisphosphate 2-kinase
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.34 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Magnesium Chloride, Sodium Acetate, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.6→57.46 Å / Num. obs: 15186 / % possible obs: 99.6 % / Redundancy: 6.6 % / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MW8

5mw8


Resolution: 2.6→57.46 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 39.012 / SU ML: 0.67 / Cross valid method: THROUGHOUT / ESU R: 1.229 / ESU R Free: 0.37 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28954 707 4.7 %RANDOM
Rwork0.25343 ---
obs0.25523 14393 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.549 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å2-12.44 Å2
2---1.02 Å20 Å2
3---6.07 Å2
Refinement stepCycle: 1 / Resolution: 2.6→57.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 37 26 3341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193390
X-RAY DIFFRACTIONr_bond_other_d0.0010.023285
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9864577
X-RAY DIFFRACTIONr_angle_other_deg0.92637592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5823.986148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69515621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9031518
X-RAY DIFFRACTIONr_chiral_restr0.070.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
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_it2.5726.8221623
X-RAY DIFFRACTIONr_mcbond_other2.5666.821622
X-RAY DIFFRACTIONr_mcangle_it4.44910.1942013
X-RAY DIFFRACTIONr_mcangle_other4.44810.1962014
X-RAY DIFFRACTIONr_scbond_it2.1627.0431767
X-RAY DIFFRACTIONr_scbond_other2.1037.0351764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.96910.4752562
X-RAY DIFFRACTIONr_long_range_B_refined7.24851.6513613
X-RAY DIFFRACTIONr_long_range_B_other7.27151.6713611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.677 37 -
Rwork0.392 1067 -
obs--99.01 %

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