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- PDB-6gfh: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in... -

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Basic information

Entry
Database: PDB / ID: 6gfh
TitleInositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with neo-IP5 and ATP
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / IPK1 / MYO-IP5
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'-TRIPHOSPHATE / neo-Inositol pentakisphosphate / Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWhitfield, H.L. / Brearley, C.A. / Hemmings, A.M.
CitationJournal: J. Med. Chem. / Year: 2018
Title: A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase.
Authors: Whitfield, H. / Gilmartin, M. / Baker, K. / Riley, A.M. / Godage, H.Y. / Potter, B.V.L. / Hemmings, A.M. / Brearley, C.A.
History
DepositionApr 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 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 / 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_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)108,57515
Polymers105,7282
Non-polymers2,84713
Water2,018112
1
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1657
Polymers52,8641
Non-polymers1,3016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4108
Polymers52,8641
Non-polymers1,5467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.632, 60.563, 84.482
Angle α, β, γ (deg.)87.810, 88.430, 63.010
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inositol-pentakisphosphate 2-kinase


Mass: 52863.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At5g40720 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A178UAB5, UniProt: Q93YN9*PLUS, inositol-pentakisphosphate 2-kinase

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Non-polymers , 7 types, 125 molecules

#2: Chemical ChemComp-K7V / neo-Inositol pentakisphosphate


Mass: 580.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H17O21P5
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18 % PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2, 25% EG or 35% PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.65→29.34 Å / Num. obs: 27766 / % possible obs: 90.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 47.33 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.11 / Rrim(I) all: 0.169 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.65-2.782.10.70536580.3480.6250.94589.9
8.79-29.342.20.0668020.9890.0520.08595.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XAM

2xam


Resolution: 2.65→29.335 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.92
RfactorNum. reflection% reflection
Rfree0.2681 1425 5.13 %
Rwork0.1993 --
obs0.2031 27753 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108 Å2 / Biso mean: 52.4975 Å2 / Biso min: 19.29 Å2
Refinement stepCycle: final / Resolution: 2.65→29.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6616 0 242 112 6970
Biso mean--55.09 44.24 -
Num. residues----830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096890
X-RAY DIFFRACTIONf_angle_d1.1769309
X-RAY DIFFRACTIONf_chiral_restr0.051036
X-RAY DIFFRACTIONf_plane_restr0.0051162
X-RAY DIFFRACTIONf_dihedral_angle_d17.7944193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6501-2.74470.2906970.25342623272089
2.7447-2.85450.34261150.26392708282392
2.8545-2.98430.36491560.27432587274390
2.9843-3.14150.38651320.2712529266187
3.1415-3.33810.34391080.24142378248682
3.3381-3.59540.3241610.21882759292096
3.5954-3.95640.25011210.18132813293495
3.9564-4.52710.23322040.16222682288694
4.5271-5.69680.22911980.16612571276991
5.6968-29.3370.21751330.16792678281192

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