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- PDB-2xal: Lead derivative of Inositol 1,3,4,5,6-pentakisphosphate 2-kinase ... -

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Basic information

Entry
Database: PDB / ID: 2xal
TitleLead derivative of Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6.
ComponentsINOSITOL-PENTAKISPHOSPHATE 2-KINASE
KeywordsTRANSFERASE / INOSITOL POLYPHOSPHATE KINASE / PHYTIC ACID SYNTHASE
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 / nucleus / metal ion binding / 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 / LEAD (II) ION / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 29, 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 1.4Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.5Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.0Oct 7, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _pdbx_validate_close_contact.auth_atom_id_2 / _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_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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)104,56912
Polymers101,4352
Non-polymers3,13410
Water00
1
A: INOSITOL-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2856
Polymers50,7181
Non-polymers1,5675
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: INOSITOL-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2856
Polymers50,7181
Non-polymers1,5675
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.063, 110.971, 138.694
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: 2

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: (0.99776, 0.05526, 0.03759), (0.05799, -0.99543, -0.07592), (0.03322, 0.07793, -0.99641)
Vector: -34.32505, 123.48315, 103.57463)

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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


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#4: 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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY
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: 2.2 Å3/Da / Density % sol: 44 %
Description: HIGH RESOLUTION DATA FROM PDB ENTRY 2XAM WAS NECESARY FOR MODEL COMPLETION AND REFINEMENT
Crystal growpH: 5.9
Details: 22% PEG 3350, 100 MM BIS-TRIS PH 5.9, SOAKING IN 100 MM LEAD ACETATE. PROTEIN WAS MIXED WITH 2 MM ADP AND 2 MM INOSITOL-6-P

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9478
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9478 Å / Relative weight: 1
ReflectionResolution: 3.2→138.69 Å / Num. obs: 15450 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.68 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.34
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data scaling
SHELXphasing
autoSHARPphasing
REFMAC5.5.0066refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.2→86.71 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.852 / SU B: 44.748 / SU ML: 0.44 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26835 768 5 %RANDOM
Rwork0.21049 ---
obs0.21335 14634 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: 21.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0 Å2
2--0.52 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 3.2→86.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6719 0 132 0 6851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.46229433
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15624.647312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.203151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5871539
X-RAY DIFFRACTIONr_chiral_restr0.0780.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215095
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_it0.4831.54203
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93326789
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.19432769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1724.52644
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
11A164tight positional0.040.05
12B164tight positional0.040.05
21A364tight positional0.050.05
22B364tight positional0.050.05
31A440tight positional0.050.05
32B440tight positional0.050.05
41A196tight positional0.040.05
42B196tight positional0.040.05
51A112tight positional0.050.05
52B112tight positional0.050.05
61A132tight positional0.040.05
62B132tight positional0.040.05
11A152medium positional0.050.5
12B152medium positional0.050.5
21A366medium positional0.070.5
22B366medium positional0.070.5
31A424medium positional0.060.5
32B424medium positional0.060.5
41A196medium positional0.060.5
42B196medium positional0.060.5
51A105medium positional0.060.5
52B105medium positional0.060.5
61A161medium positional0.070.5
62B161medium positional0.070.5
11A164tight thermal0.180.5
12B164tight thermal0.180.5
21A364tight thermal0.280.5
22B364tight thermal0.280.5
31A440tight thermal0.220.5
32B440tight thermal0.220.5
41A196tight thermal0.30.5
42B196tight thermal0.30.5
51A112tight thermal0.280.5
52B112tight thermal0.280.5
61A132tight thermal0.240.5
62B132tight thermal0.240.5
11A152medium thermal0.212
12B152medium thermal0.212
21A366medium thermal0.332
22B366medium thermal0.332
31A424medium thermal0.252
32B424medium thermal0.252
41A196medium thermal0.322
42B196medium thermal0.322
51A105medium thermal0.332
52B105medium thermal0.332
61A161medium thermal0.262
62B161medium thermal0.262
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 56 -
Rwork0.265 1072 -
obs--99.65 %
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)
12.08931.1029-0.93562.0364-1.6023.3032-0.08430.1255-0.1067-0.20550.0416-0.05730.28830.19640.04270.03340.0164-0.00030.0384-0.01150.009940.307869.112430.538
23.8723-0.9067-0.98044.06310.66032.17-0.2672-0.09530.02260.14830.2112-0.08920.07120.04270.05610.04860.0282-0.01310.0223-0.01060.007769.146153.458779.731
30.68370.0736-0.00062.0031-0.50990.83130.0456-0.0131-0.04050.08260.00880.1356-0.1112-0.0131-0.05430.0344-0.00480.0120.0024-0.00060.015528.865472.702148.6354
41.16270.01220.10492.2881-0.07650.7664-0.0350.12080.0667-0.0588-0.06330.05320.0177-0.12510.09830.0456-0.0047-0.01610.1008-0.01130.021558.388650.494960.465
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 DIFFRACTION4B161 - 435

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