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

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Basic information

Entry
Database: PDB / ID: 2xar
TitleInositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP6.
ComponentsINOSITOL-PENTAKISPHOSPHATE 2-KINASE
KeywordsTRANSFERASE / IPK / INSP5 2-K / PHYTIC ACID SYNTHASE
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
INOSITOL HEXAKISPHOSPHATE / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGonzalez, B. / Banos-Sanz, J.I. / Villate, M. / Brearley, C.A. / Sanz-Aparicio, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase is a Distant Ipk Member with a Singular Inositide Binding Site for Axial 2-Oh Recognition.
Authors: Gonzalez, B. / Banos-Sanz, J.I. / Villate, M. / Brearley, C.A. / Sanz-Aparicio, J.
History
DepositionMar 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Non-polymer description / Other / Version format compliance
Revision 1.2Mar 7, 2012Group: Other
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
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
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)102,8866
Polymers101,4352
Non-polymers1,4514
Water0
1
A: INOSITOL-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4433
Polymers50,7181
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: INOSITOL-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4433
Polymers50,7181
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.670, 112.501, 139.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUARGARGAA5 - 455 - 45
21LEULEUARGARGBB5 - 455 - 45
12VALVALSERSERAA60 - 15060 - 150
22VALVALSERSERBB60 - 15060 - 150
13CYSCYSALAALAAA162 - 271162 - 271
23CYSCYSALAALABB162 - 271162 - 271
14HISHISCYSCYSAA282 - 330282 - 330
24HISHISCYSCYSBB282 - 330282 - 330
15PROPROGLNGLNAA349 - 376349 - 376
25PROPROGLNGLNBB349 - 376349 - 376
16ASPASPARGARGAA400 - 432400 - 432
26ASPASPARGARGBB400 - 432400 - 432

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper: (Code: given
Matrix: (0.99869, 0.04544, 0.02363), (0.04719, -0.9957, -0.07972), (0.01991, 0.08073, -0.99654)
Vector: -32.77592, 126.54977, 104.96889)

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


Mass: 50717.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PKLSLT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHERE ARE SEVERAL DISCREPANCES IN SEQUENCE BETWEEN THE DATABASE ANNOTATION AND THE CRYSTALLISED PROTEIN

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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: 2.23 Å3/Da / Density % sol: 44.78 % / Description: NONE
Crystal growpH: 5.9
Details: 22% PEG 3350, 100 MM BIS-TRIS PH 5.9 2MM MGCL2. PROTEIN WAS MIXED WITH 2 MM INOSITOL-6-P

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→112.5 Å / Num. obs: 17187 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.63 % / Biso Wilson estimate: 67.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.76
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.78 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XAM

2xam


Resolution: 3.1→112.5 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.838 / SU B: 56.369 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.29888 870 5.1 %RANDOM
Rwork0.23803 ---
obs0.24103 16316 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2--0.92 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 3.1→112.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6677 0 74 0 6751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226869
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9899278
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1315832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59724.63311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.371151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3331539
X-RAY DIFFRACTIONr_chiral_restr0.0740.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215045
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_it0.4291.54178
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80926741
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.84132691
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5564.52537
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A316tight positional0.020.05
21A730tight positional0.030.05
31A864tight positional0.040.05
41A392tight positional0.030.05
51A217tight positional0.040.05
61A293tight positional0.030.05
12B316tight thermal0.120.5
22B730tight thermal0.130.5
32B864tight thermal0.120.5
42B392tight thermal0.10.5
52B217tight thermal0.10.5
62B293tight thermal0.130.5
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 60 -
Rwork0.306 1185 -
obs--100 %
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)
13.35552.4374-1.69843.8894-2.30752.26910.19220.2143-0.1221-0.4816-0.2532-0.40260.43780.3180.06110.32940.05950.02880.39040.01190.09939.909270.437630.6362
23.7897-0.91570.52582.94660.39092.9536-0.2076-0.02990.07680.53820.155-0.19480.08570.12360.05260.11790.0175-0.03460.1027-0.04210.02968.83754.113680.3786
31.0361-0.32680.33064.8896-1.05851.01090.12570.05270.0180.0924-0.07310.164-0.1030.045-0.05260.0821-0.03660.01850.0696-0.01740.053128.725474.102848.8706
42.1321-0.08350.33943.83430.01261.3242-0.06720.23630.1352-0.1435-0.09270.19430.05240.0170.15990.0529-0.0292-0.04460.18160.00480.075958.092851.147960.9514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 150
2X-RAY DIFFRACTION2B3 - 150
3X-RAY DIFFRACTION3A160 - 435
4X-RAY DIFFRACTION4B160 - 435

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