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- PDB-5mw8: INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN... -

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Basic information

Entry
Database: PDB / ID: 5mw8
TitleINOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH ATP and IP5
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / protein structure / mammal IPK / inositol kinase
Function / homology
Function and homology information


Synthesis of IPs in the nucleus / Synthesis of pyrophosphates in the cytosol / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / inositol phosphate biosynthetic process / 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
MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE / ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)55,1067
Polymers53,8461
Non-polymers1,2606
Water70339
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-24 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.162, 71.495, 61.197
Angle α, β, γ (deg.)90.00, 111.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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 (E. coli) / Strain (production host): BL21(de3) / Variant (production host): star
References: UniProt: Q6P1C1, inositol-pentakisphosphate 2-kinase

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Non-polymers , 6 types, 45 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-5MY / MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE


Mass: 580.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H17O21P5
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting 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 / Details: KB focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.4→71.5 Å / Num. obs: 18528 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.5 / CC1/2: 0.967 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
Cootmodel building
PHENIXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→56.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 20.936 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.296 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27117 938 5.1 %RANDOM
Rwork0.24101 ---
obs0.24252 17573 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.289 Å2
Baniso -1Baniso -2Baniso -3
1-5.67 Å20 Å2-9.42 Å2
2---1.88 Å20 Å2
3---2.74 Å2
Refinement stepCycle: 1 / Resolution: 2.4→56.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 70 39 3443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193481
X-RAY DIFFRACTIONr_bond_other_d0.0010.023351
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9924706
X-RAY DIFFRACTIONr_angle_other_deg0.86937746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82823.947152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03515637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2761520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
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_it1.4565.221655
X-RAY DIFFRACTIONr_mcbond_other1.4575.2191653
X-RAY DIFFRACTIONr_mcangle_it2.6327.8062057
X-RAY DIFFRACTIONr_mcangle_other2.6327.8072058
X-RAY DIFFRACTIONr_scbond_it1.1675.3491826
X-RAY DIFFRACTIONr_scbond_other1.1675.3491827
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1437.9622650
X-RAY DIFFRACTIONr_long_range_B_refined4.54939.3433700
X-RAY DIFFRACTIONr_long_range_B_other4.51639.3653688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 75 -
Rwork0.405 1319 -
obs--99.64 %

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