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

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Basic information

Entry
Database: PDB / ID: 6fjk
TitleInositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with myo-IP6 and ADP
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / IPK1 / MYO-IP6
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 / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.025 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 22, 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 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_remark ...audit_author / database_PDB_remark / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _database_PDB_remark.text
Revision 2.0Oct 7, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _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_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 17, 2024Group: 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)108,22812
Polymers105,7282
Non-polymers2,50010
Water8,143452
1
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0415
Polymers52,8641
Non-polymers1,1774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1877
Polymers52,8641
Non-polymers1,3236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.810, 60.340, 83.980
Angle α, β, γ (deg.)88.530, 89.180, 63.360
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) / Strain (production host): ROSETTA
References: UniProt: A0A178UAB5, UniProt: Q93YN9*PLUS, inositol-pentakisphosphate 2-kinase

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Non-polymers , 6 types, 462 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H18O24P6 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IPK1 At5g42810 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: inositol-pentakisphosphate 2-kinase
#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-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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.71 Å3/Da / Density % sol: 54.57 % / Description: PLATE
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: Sep 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.025→83.952 Å / Num. obs: 61224 / % possible obs: 89.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.57 Å2 / Rpim(I) all: 0.07 / Rrim(I) all: 0.099 / Rsym value: 0.068 / Net I/av σ(I): 4.1 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.025-2.0820.2193.545910.4130.5840.21989.9
2.08-2.1320.1664.743630.3360.4760.16688.4
2.13-2.220.155.241430.2820.3980.1587.4
2.2-2.261.90.135.938480.2290.3240.1381.9
2.26-2.341.90.1027.438650.1750.2480.10285
2.34-2.4220.0938.140100.1530.2170.09392.7
2.42-2.5120.0789.539280.1280.1810.07892.9
2.51-2.6120.0759.837700.1180.1670.07592.5
2.61-2.7320.0710.135340.10.1410.0792.1
2.73-2.8620.0611233720.0880.1240.06190.9
2.86-3.021.90.06210.832050.0810.1140.06290.2
3.02-3.21.90.0611.528940.0730.1030.0687
3.2-3.421.90.0625.525640.060.0840.06282.5
3.42-3.720.05212.327830.0560.0790.05294.6
3.7-4.0520.04913.625320.0530.0740.04994.4
4.05-4.5320.04215.722830.0480.0690.04293.7
4.53-5.231.90.0595.919630.0460.0650.05991.8
5.23-6.41.90.05413.515150.0450.0640.05483.8
6.4-9.0620.093.213160.0430.0610.0994.2
9.06-83.95220.05412.47450.0320.0450.05497.7

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Processing

Software
NameClassification
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XAM

2xam


Resolution: 2.025→83.952 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 24.33
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 3100 5.07 %RANDOM SELECTION
Rwork0.1779 ---
obs0.1803 61203 89.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.97 Å2 / Biso mean: 40.5667 Å2 / Biso min: 12.29 Å2
Refinement stepCycle: final / Resolution: 2.025→83.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6675 0 187 452 7314
Biso mean--37.79 40.58 -
Num. residues----840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076931
X-RAY DIFFRACTIONf_angle_d0.9619373
X-RAY DIFFRACTIONf_chiral_restr0.0481044
X-RAY DIFFRACTIONf_plane_restr0.0051175
X-RAY DIFFRACTIONf_dihedral_angle_d12.6664218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.025-2.05660.30611480.24522686283490
2.0566-2.09030.27831400.22422671281190
2.0903-2.12640.29241390.21482570270988
2.1264-2.16510.24641440.21672589273389
2.1651-2.20670.32861400.21792529266986
2.2067-2.25180.27841260.20752435256183
2.2518-2.30070.29571170.19482308242577
2.3007-2.35420.23441360.18532672280892
2.3542-2.41310.23311520.18292797294993
2.4131-2.47840.21551530.17762706285993
2.4784-2.55130.25031450.17612749289492
2.5513-2.63370.25421370.17722731286892
2.6337-2.72780.21751470.18042708285592
2.7278-2.8370.22151260.18332718284491
2.837-2.96610.25651480.19572627277591
2.9661-3.12250.221430.18962602274589
3.1225-3.31820.2221290.1812387251680
3.3182-3.57440.211600.16722706286693
3.5744-3.93410.22781370.15892809294694
3.9341-4.50330.17581560.14632748290494
4.5033-5.67350.1881390.1612687282691
5.6735-84.02410.21741380.18182668280690
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0091-0.47880.84350.8337-0.26852.3404-0.0761-0.592-0.36040.36860.08020.01270.38790.1834-0.00960.4374-0.0171-0.02560.43750.09740.235616.2517-0.876635.1752
21.6543-0.0191-1.77370.6918-0.23551.8973-0.00260.0317-0.34760.0992-0.0421-0.150.1097-0.14150.04430.21590.007-0.00990.27560.02760.313520.8115-1.39910.9452
32.4665-1.2051-0.46155.18020.7052.8021-0.2327-0.62480.02570.61730.4-0.33990.06660.4295-0.14410.2243-0.0009-0.06920.3557-0.01590.252124.42339.919718.216
42.685-0.24761.40142.229-0.10412.33460.1921-0.1175-0.41780.37550.03880.11220.30450.2105-0.18680.3288-0.0128-0.00660.28210.04540.216810.0198-4.655424.0628
51.7519-0.2106-0.43311.6536-0.2441.61250.024-0.07580.19260.1943-0.09060.2896-0.20940.04780.02280.1983-0.0294-0.00320.1174-0.0490.26224.153917.80610.3655
61.79470.1257-0.1692.80841.18732.34370.0426-0.02530.32390.093-0.04150.4772-0.2694-0.38760.02830.25770.04320.04240.2115-0.05330.364-2.618922.411113.6137
72.11280.03890.50611.11670.62442.68270.0049-0.55420.27550.6735-0.13310.7012-0.3695-0.45690.09070.48530.03510.21320.4097-0.10970.4299-4.975920.06327.475
82.7025-1.0819-1.14382.6880.08333.09130.15760.34950.0606-0.3201-0.0787-0.09580.15510.2192-0.1140.22910.0027-0.02440.19470.00320.17217.533814.4034-3.0674
91.3992-0.6048-1.02692.9110.6823.1535-0.0944-0.46730.15540.56780.08650.1615-0.09420.1477-0.04750.273-0.0181-0.01530.2483-0.08360.197712.593719.687519.222
106.1896-0.6751.51242.6258-0.29713.9822-0.14320.3835-0.4133-0.45150.21590.41060.078-0.4327-0.1130.2253-0.0779-0.06370.20020.00970.26671.935110.4758-3.2895
110.7982-0.44561.02620.1952-0.51611.10290.04760.6075-0.2955-0.37560.04310.2460.1769-0.0677-0.1270.48990.0645-0.12590.74710.01070.2545-23.4294-13.7765-35.8973
121.1837-0.1527-0.64890.8661.21323.28660.10930.1803-0.001-0.2698-0.16310.29840.0728-0.0124-0.01670.26410.0555-0.06250.33840.00080.2731-25.0548-9.9448-12.4156
133.49690.44140.46712.3016-0.60471.89060.33420.69530.1831-0.2528-0.3156-0.1068-0.2705-0.47820.0170.32610.1457-0.03270.38980.0430.3145-20.2287-0.8924-18.5565
142.0386-0.85380.53560.8229-0.8971.92630.19020.5147-0.3651-0.4588-0.03240.40320.3855-0.5249-0.030.41280.0139-0.11130.5398-0.0910.3399-23.2313-21.0479-24.8105
151.8236-0.93710.03621.56530.64272.27880.10040.31250.0724-0.1738-0.1273-0.2686-0.10520.26260.04810.1531-0.00890.04890.22760.03760.2322-2.2526-12.6639-8.8634
162.0307-0.3779-0.90021.92760.23352.10870.01260.18470.2186-0.192-0.0348-0.67840.0230.37680.00580.19450.01710.06650.31530.06320.34635.5658-15.2822-12.9993
171.8478-0.2348-0.39091.83050.3422.62550.17470.62480.006-0.5557-0.2093-0.37650.04610.54480.00110.41710.12490.1330.52080.03710.35565.5685-18.4196-26.9384
183.5935-0.6943-1.04142.06481.00152.38260.0052-0.34180.27040.06790.0978-0.11470.05090.154-0.01870.1472-0.0068-0.02340.13050.00510.2047-13.7659-3.94383.2688
197.2552-3.30012.00085.1523-1.37083.2477-0.0415-0.4408-0.67260.32190.14230.15860.12680.0664-0.09720.2087-0.038-0.01660.16530.03010.2401-7.6231-18.67723.2156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 36 )A-6 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 72 )A37 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 105 )A73 - 105
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 147 )A106 - 147
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 202 )A148 - 202
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 234 )A203 - 234
7X-RAY DIFFRACTION7chain 'A' and (resid 235 through 298 )A235 - 298
8X-RAY DIFFRACTION8chain 'A' and (resid 299 through 349 )A299 - 349
9X-RAY DIFFRACTION9chain 'A' and (resid 350 through 412 )A350 - 412
10X-RAY DIFFRACTION10chain 'A' and (resid 413 through 437 )A413 - 437
11X-RAY DIFFRACTION11chain 'B' and (resid -6 through 36 )B-6 - 36
12X-RAY DIFFRACTION12chain 'B' and (resid 37 through 72 )B37 - 72
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 105 )B73 - 105
14X-RAY DIFFRACTION14chain 'B' and (resid 106 through 147 )B106 - 147
15X-RAY DIFFRACTION15chain 'B' and (resid 148 through 202 )B148 - 202
16X-RAY DIFFRACTION16chain 'B' and (resid 203 through 234 )B203 - 234
17X-RAY DIFFRACTION17chain 'B' and (resid 235 through 298 )B235 - 298
18X-RAY DIFFRACTION18chain 'B' and (resid 299 through 349 )B299 - 349
19X-RAY DIFFRACTION19chain 'B' and (resid 413 through 437 )B413 - 437

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