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

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Basic information

Entry
Database: PDB / ID: 5mwl
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 pentakisphosphate 2-kinase activity / inositol phosphate biosynthetic process / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / molecular adaptor activity / phosphorylation / nucleolus / ATP binding ...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 / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / molecular adaptor activity / phosphorylation / nucleolus / 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 / ADENOSINE-5'-TRIPHOSPHATE / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.3Jan 17, 2024Group: 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,08910
Polymers107,6922
Non-polymers1,3978
Water543
1
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1137
Polymers53,8461
Non-polymers1,2676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9773
Polymers53,8461
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.623, 140.758, 68.662
Angle α, β, γ (deg.)90.00, 106.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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

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Non-polymers , 5 types, 11 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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.: 4 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.68 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25 / Details: Magnesium chloride, MES, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.2→70.38 Å / Num. obs: 19318 / % possible obs: 99.3 % / Redundancy: 6.9 % / Net I/σ(I): 14.7

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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: 3.2→70.38 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.91 / SU B: 24.974 / SU ML: 0.414 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24529 918 4.8 %RANDOM
Rwork0.22513 ---
obs0.22614 18378 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 102.045 Å2
Baniso -1Baniso -2Baniso -3
1-7.11 Å20 Å23.1 Å2
2---4.73 Å20 Å2
3----3.58 Å2
Refinement stepCycle: 1 / Resolution: 3.2→70.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6574 0 69 3 6646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196780
X-RAY DIFFRACTIONr_bond_other_d0.0010.026568
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9779148
X-RAY DIFFRACTIONr_angle_other_deg0.867315154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25424.079304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.047151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8821535
X-RAY DIFFRACTIONr_chiral_restr0.0640.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021533
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_it3.40510.1313247
X-RAY DIFFRACTIONr_mcbond_other3.40410.133246
X-RAY DIFFRACTIONr_mcangle_it5.87215.1864036
X-RAY DIFFRACTIONr_mcangle_other5.87215.1874037
X-RAY DIFFRACTIONr_scbond_it2.82910.4713533
X-RAY DIFFRACTIONr_scbond_other2.82610.4643529
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.03915.5785107
X-RAY DIFFRACTIONr_long_range_B_refined9.21178.3427146
X-RAY DIFFRACTIONr_long_range_B_other9.21178.3547147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 72 -
Rwork0.298 1338 -
obs--98.19 %

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