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- PDB-4lv7: Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinas... -

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Basic information

Entry
Database: PDB / ID: 4lv7
TitleCrystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / ipk / ins5p 2-k / atipk1 / ip5 2-k / inositol phosphorylation
Function / homology
Function and homology information


inositol tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium ...inositol tetrakisphosphate 2-kinase activity / inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium / phosphorylation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGosein, V. / Miller, G.J.
CitationJournal: J. Biol. Chem. / Year: 2013
Title: Conformational stability of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) dictates its substrate selectivity.
Authors: Gosein, V. / Miller, G.J.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 14, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.pdbx_synonyms / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,99710
Polymers110,6432
Non-polymers2,3548
Water0
1
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4995
Polymers55,3221
Non-polymers1,1774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4995
Polymers55,3221
Non-polymers1,1774
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.763, 59.353, 82.232
Angle α, β, γ (deg.)83.010, 89.920, 63.410
Int Tables number1
Space group name H-MP1

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Components

#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: 55321.730 Da / Num. of mol.: 2 / Mutation: E82C, S142C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g42810, IPK1, MJB21.19 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: Q93YN9, inositol-pentakisphosphate 2-kinase
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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

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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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.08M MES, 19.85% PEG3000, 0.17M NaCl, 2.35% benzamidine HCl, Protein: 5mg/mL, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 4, 2012 / Details: VariMax HF
RadiationMonochromator: Confocal dual reflection mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32955 / % possible obs: 95.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 30.89 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.259 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.543.40.31511660.788169.4
2.54-2.593.40.32214790.78183.7
2.59-2.643.70.28416240.786196.2
2.64-2.693.90.27716690.881195.4
2.69-2.7540.24316610.874195.7
2.75-2.8240.22116930.988196.2
2.82-2.8940.22516410.964196.1
2.89-2.9640.19517140.952196.4
2.96-3.0540.18316311.049196.5
3.05-3.1540.15417061.119196.3
3.15-3.2640.13416431.25197.6
3.26-3.3940.11816961.386197.2
3.39-3.5540.10316841.446197.2
3.55-3.7340.09317251.586197.7
3.73-3.9740.08716901.57198.1
3.97-4.273.90.07916891.742198.1
4.27-4.73.90.07316931.893198.5
4.7-5.383.90.07117301.734198.6
5.38-6.783.90.07117111.599199.1
6.78-503.90.04417101.348198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_473refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2XAM

2xam


Resolution: 2.6→34.548 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7495 / SU ML: 0.43 / σ(F): 0.04 / Phase error: 32.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2943 1748 6.09 %RANDOM
Rwork0.2244 ---
obs0.2287 28726 93.4 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.419 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 86.07 Å2 / Biso mean: 32.8169 Å2 / Biso min: 6.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.9547 Å21.2256 Å2-0.3169 Å2
2---1.128 Å2-6.4045 Å2
3---0.1733 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 130 0 6380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0226506
X-RAY DIFFRACTIONf_angle_d1.328795
X-RAY DIFFRACTIONf_chiral_restr0.074989
X-RAY DIFFRACTIONf_plane_restr0.0051087
X-RAY DIFFRACTIONf_dihedral_angle_d20.182530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.69290.38141700.2862486265687
2.6929-2.80070.36541650.27932563272888
2.8007-2.92810.40411570.28522548270588
2.9281-3.08240.38971710.28042594276590
3.0824-3.27530.34351760.2572756293295
3.2753-3.5280.29681810.23152789297097
3.528-3.88260.29311800.19972801298197
3.8826-4.44340.25141840.17482802298697
4.4434-5.59440.22771830.18982803298697
5.5944-34.55110.23851810.21792836301798

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