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- PDB-6fl8: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in... -

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Basic information

Entry
Database: PDB / ID: 6fl8
TitleInositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with purpurogallin and ADP
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / IPK1 / PURPUROGALLIN / ADP
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 / 2,3,4,6-tetrahydroxy-5H-benzo[7]annulen-5-one / Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJan 25, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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)107,72118
Polymers105,7282
Non-polymers1,99316
Water4,756264
1
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7257
Polymers52,8641
Non-polymers8616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,99611
Polymers52,8641
Non-polymers1,13210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.990, 61.450, 83.430
Angle α, β, γ (deg.)89.55, 88.00, 62.08
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, 280 molecules

#2: Chemical ChemComp-TIY / 2,3,4,6-tetrahydroxy-5H-benzo[7]annulen-5-one / Purpurogallin


Mass: 220.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O5
#3: Chemical ChemComp-ADP / ADENOSINE-5'-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.: 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 52.11 %
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: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.1→54.29 Å / Num. obs: 55908 / % possible obs: 91 % / Redundancy: 2.3 % / Biso Wilson estimate: 38.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.066 / Rrim(I) all: 0.104 / Net I/σ(I): 6.3 / Num. measured all: 129143 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.3 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.150.67541990.5270.5650.88492.1
9.39-54.290.0386670.9930.0310.04997.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimless0.5.23data scaling
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XAM

2xam


Resolution: 2.1→54.295 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 2765 4.95 %
Rwork0.1983 --
obs0.2007 55881 90.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→54.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6721 0 123 264 7108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086964
X-RAY DIFFRACTIONf_angle_d0.9689394
X-RAY DIFFRACTIONf_dihedral_angle_d13.7634213
X-RAY DIFFRACTIONf_chiral_restr0.0511037
X-RAY DIFFRACTIONf_plane_restr0.0061187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13620.40211360.32482733X-RAY DIFFRACTION92
2.1362-2.17510.33971610.29572617X-RAY DIFFRACTION92
2.1751-2.21690.34231610.2812684X-RAY DIFFRACTION92
2.2169-2.26210.3481540.26762645X-RAY DIFFRACTION91
2.2621-2.31130.29511460.24632624X-RAY DIFFRACTION90
2.3113-2.36510.31661300.24562564X-RAY DIFFRACTION88
2.3651-2.42430.3149910.23662423X-RAY DIFFRACTION83
2.4243-2.48980.27961190.22922789X-RAY DIFFRACTION94
2.4898-2.56310.31121620.21972718X-RAY DIFFRACTION94
2.5631-2.64580.27531480.2182709X-RAY DIFFRACTION93
2.6458-2.74030.25521010.21612738X-RAY DIFFRACTION92
2.7403-2.85010.28171170.21282702X-RAY DIFFRACTION92
2.8501-2.97980.26081950.21812599X-RAY DIFFRACTION90
2.9798-3.13680.2631590.2142415X-RAY DIFFRACTION84
3.1368-3.33340.22981020.2072781X-RAY DIFFRACTION94
3.3334-3.59070.2593900.1912821X-RAY DIFFRACTION95
3.5907-3.95190.26041600.18262681X-RAY DIFFRACTION93
3.9519-4.52350.21690.16222542X-RAY DIFFRACTION88
4.5235-5.69820.20961240.16712673X-RAY DIFFRACTION91
5.6982-54.3130.18061400.16782658X-RAY DIFFRACTION91

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