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- PDB-4aqk: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with ADP... -

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Basic information

Entry
Database: PDB / ID: 4aqk
TitleInositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with ADP and IP6
ComponentsINOSITOL-PENTAKISPHOSPHATE 2-KINASE
KeywordsTRANSFERASE / INOSITIDE KINASE / PHYTIC ACID / INOSITIDE SIGNALLING / INSP5 2-K
Function / homology
Function and homology information


inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-1,3,4,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / phosphate ion homeostasis / intracellular phosphate ion homeostasis / defense response to fungus / defense response to virus ...inositol-1,4,5,6-tetrakisphosphate 2-kinase activity / inositol-1,3,4,6-tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / phosphate ion homeostasis / intracellular phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inositol-pentakisphosphate 2-kinase, N-lobe / Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase, N-terminal lobe / Inositol-pentakisphosphate 2-kinase / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsI Banos-Sanz, J. / Sanz-Aparicio, J. / Gonzalez, B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Apo Form of Insp5 2-K from Arabidopsis Thaliana.
Authors: Banos-Sanz, J.I. / Sanz-Aparicio, J. / Brearley, C.A. / Gonzalez, B.
History
DepositionApr 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 2.0Oct 7, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
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_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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_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_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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: INOSITOL-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4985
Polymers51,3211
Non-polymers1,1774
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.110, 65.660, 121.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / 3 / 4 / 5 / 6)P5 2-KINASE / ATIPK1 ...INOSITOL-1 / 3 / 4 / 5 / 6-PENTAKISPHOSPHATE 2-KINASE / INS(1 / 3 / 4 / 5 / 6)P5 2-KINASE / ATIPK1 / INSP5 2-KINASE


Mass: 51321.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q93YN9, inositol-pentakisphosphate 2-kinase

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Non-polymers , 5 types, 64 molecules

#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.45 Å3/Da / Density % sol: 49.77 % / Description: NONE
Crystal growpH: 5.9 / Details: 22% PEG 3350, BIS-TRIS PH 5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→62.11 Å / Num. obs: 20463 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.1 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XAN

2xan


Resolution: 2.4→60.9 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.852 / SU B: 11.004 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.522 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29215 984 5.1 %RANDOM
Rwork0.24392 ---
obs0.2463 18278 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.452 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--4.18 Å20 Å2
3----3.52 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 65 60 3422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1332.0024626
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0915410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16424.416154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17415628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7481521
X-RAY DIFFRACTIONr_chiral_restr0.0650.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212504
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3621.52058
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68423321
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.82631363
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4874.51305
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.3 73 -
Rwork0.301 1223 -
obs--89.56 %

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