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

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Basic information

Entry
Database: PDB / ID: 2xan
Titleinositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with AMP PNP and IP5
ComponentsINOSITOL-PENTAKISPHOSPHATE 2-KINASE
KeywordsTRANSFERASE / PHYTIC ACID SYNTHASE / IP6
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
MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Mar 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)103,78710
Polymers101,4352
Non-polymers2,3528
Water4,666259
1
A: INOSITOL-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8945
Polymers50,7181
Non-polymers1,1764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: INOSITOL-PENTAKISPHOSPHATE 2-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8945
Polymers50,7181
Non-polymers1,1764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.418, 113.429, 140.472
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

NCS domain segments:

Component-ID: 1 / Refine code: 4

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

NCS ensembles :
ID
1
2
3
4
5

NCS oper: (Code: given
Matrix: (0.99907, 0.04084, 0.01363), (0.03973, -0.99649, 0.07373), (0.01659, -0.07312, -0.99718)
Vector: 25.16859, 120.69994, 115.69789)

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 267 molecules

#2: Chemical ChemComp-5MY / MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE


Mass: 580.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H17O21P5
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHERE ARE SEVERAL DISCREPANCIES BETWEEN THE UNIPROT DATABASE AND THE CRYSTALLISED PROTEIN SEQUENCE

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 5.9
Details: 22% PEG 3350, 100 MM BIS-TRIS, PH 5.9 PROTEIN WAS MIXED WITH 2 MM AMP PNP AND 2 MM INOSITOL-5-P

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.2→88.25 Å / Num. obs: 47247 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XAM

2xam


Resolution: 2.2→140.03 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.962 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.246 / 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
Rfree0.27739 2389 5.1 %RANDOM
Rwork0.22427 ---
obs0.22693 44857 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2---0.96 Å2-0 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→140.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 130 259 6979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226852
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.09529271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99424.656305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.798151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6841537
X-RAY DIFFRACTIONr_chiral_restr0.0640.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215009
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_it0.4561.54134
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86726672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.21832718
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0394.52599
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
11A316medium positional0.330.5
12B316medium positional0.330.5
21A730medium positional0.490.5
22B730medium positional0.490.5
31A864medium positional0.360.5
32B864medium positional0.360.5
41A392medium positional0.280.5
42B392medium positional0.280.5
51A217medium positional0.350.5
52B217medium positional0.350.5
11A316medium thermal0.412
12B316medium thermal0.412
21A730medium thermal0.42
22B730medium thermal0.42
31A864medium thermal0.482
32B864medium thermal0.482
41A392medium thermal0.552
42B392medium thermal0.552
51A217medium thermal0.562
52B217medium thermal0.562
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 174 -
Rwork0.239 3235 -
obs--98.9 %
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)
10.67650.9451-0.79232.2434-1.5021.4238-0.10690.0958-0.0464-0.44860.0126-0.15690.3910.10240.09420.20540.05620.03490.13720.00270.012539.411971.291930.5485
21.6427-0.3390.20661.24250.27451.0588-0.0847-0.19080.07610.13740.0458-0.03840.05050.10030.03890.01980.0134-0.00680.0383-0.00380.006567.874153.878380.7298
30.35180.18510.01951.8797-0.32040.30120.03730.010.0580.05510.01560.1081-0.0377-0.0428-0.05280.0244-0.00050.010.0220.00850.031228.605674.710349.1076
41.2009-0.02040.38271.3618-0.02350.6574-0.09470.13730.1745-0.067-0.05490.0624-0.06090.00220.14960.0191-0.0154-0.03140.03820.02340.057357.512451.62461.2976
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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