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Basic information

Entry
Database: PDB / ID: 5w2i
TitleCrystal structure of the core catalytic domain of human inositol phosphate multikinase soaked with C4-analogue of PtdIns(4,5)P2 and ADP
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-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity ...inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-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
ADENOSINE-5'-DIPHOSPHATE / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol polyphosphate multikinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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 2.0Dec 20, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 3.0Jan 17, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 3.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_label_atom_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 polyphosphate multikinase,Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3235
Polymers29,4271
Non-polymers8964
Water3,279182
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)78.090, 78.090, 86.320
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-809-

HOH

21A-877-

HOH

31A-920-

HOH

41A-968-

HOH

51A-977-

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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H15O15P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 44.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structures, the apo crystal were further soaked under 35% (w/v) ...Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structures, the apo crystal were further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 20 mM C4-analogue of PtdIns(4,5)P2, 10 mM Mg and 5mM ATP for 1 day.

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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: Aug 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36175 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 22.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→34.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.64 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21525 1813 5.1 %RANDOM
Rwork0.16922 ---
obs0.17148 34007 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2---0.07 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.6→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 53 182 2178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192153
X-RAY DIFFRACTIONr_bond_other_d0.0010.021977
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9972947
X-RAY DIFFRACTIONr_angle_other_deg0.75334583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48424.18498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8715363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.098159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
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_it1.2590.8141019
X-RAY DIFFRACTIONr_mcbond_other1.2560.8131018
X-RAY DIFFRACTIONr_mcangle_it1.7921.2141293
X-RAY DIFFRACTIONr_mcangle_other1.7931.2151294
X-RAY DIFFRACTIONr_scbond_it1.8071.1181133
X-RAY DIFFRACTIONr_scbond_other1.7941.1111129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1261.5871649
X-RAY DIFFRACTIONr_long_range_B_refined4.8618.3982646
X-RAY DIFFRACTIONr_long_range_B_other3.9447.9642587
X-RAY DIFFRACTIONr_rigid_bond_restr1.47534129
X-RAY DIFFRACTIONr_sphericity_free34.306552
X-RAY DIFFRACTIONr_sphericity_bonded13.19654195
LS refinement shellResolution: 1.595→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 125 -
Rwork0.187 2180 -
obs--88.11 %
Refinement TLS params.Method: refined / Origin x: 3.4707 Å / Origin y: 18.1615 Å / Origin z: 26.1254 Å
111213212223313233
T0.0163 Å20.0087 Å2-0.0025 Å2-0.0421 Å20.0209 Å2--0.0199 Å2
L1.5617 °2-0.1543 °2-0.482 °2-0.854 °20.0515 °2--1.1648 °2
S-0.0738 Å °-0.0087 Å °-0.0105 Å °0.036 Å °0.08 Å °-0.0117 Å °-0.0257 Å °0.0094 Å °-0.0063 Å °

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