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

ID or keywords:

Entry

Database: PDB / ID: 2xal

Title

Lead derivative of Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6.

Components

INOSITOL-PENTAKISPHOSPHATE 2-KINASE

Keywords

TRANSFERASE / INOSITOL POLYPHOSPHATE KINASE / PHYTIC ACID SYNTHASE

Function / homology

Function and homology information

inositol-1,4,5,6-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 / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.2 Å

Authors

Gonzalez, B. / Banos-Sanz, J.I. / Villate, M. / Brearley, C.A. / Sanz-Aparicio, J.

Citation

Journal: 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

Deposition	Mar 31, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 29, 2012	Group: Other
Revision 1.3	Mar 7, 2018	Group: 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 1.4	Oct 30, 2019	Group: 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 1.5	Nov 20, 2019	Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.0	Oct 7, 2020	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2xal.cif.gz	176.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2xal.ent.gz	147.9 KB	Display	PDB format
PDBx/mmJSON format	2xal.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2xal_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	2xal_full_validation.pdf.gz	2.1 MB	Display
Data in XML	2xal_validation.xml.gz	39.6 KB	Display
Data in CIF	2xal_validation.cif.gz	52.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xa/2xal ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xal	HTTPS FTP

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Related structure data

Related structure data	2xamC 2xanC 2xaoC 2xarC C: citing same article (ref.)
Similar structure data	2xar-1 2xan-1 3a8u-d 2xao-2 4uhn-d 6gnh-d 3h4j-1 2xam-1 4a33-d 2xao-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#196 - Apr 2016 Lead Poisoning similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #56 - Aug 2004 Caspases similarity (1) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #225 - Sep 2018 Phytase similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1) #88 - Apr 2007 Clathrin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#196 - Apr 2016
Lead Poisoning
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#56 - Aug 2004
Caspases
similarity (1)
#110 - Feb 2009
Auxin and TIR1 Ubiquitin Ligase
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#218 - Feb 2018
EPSP Synthase and Weedkillers
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)

Deposited unit

A: INOSITOL-PENTAKISPHOSPHATE 2-KINASE

B: INOSITOL-PENTAKISPHOSPHATE 2-KINASE

hetero molecules

105 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: INOSITOL-PENTAKISPHOSPHATE 2-KINASE

hetero molecules

defined by author&software
52.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: INOSITOL-PENTAKISPHOSPHATE 2-KINASE

hetero molecules

defined by author&software
52.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B
1	5	A
2	5	B
1	6	A
2	6	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	5 - 45
2	1	1	2	B	5 - 45
1	1	2	2	A	60 - 150
2	1	2	2	B	60 - 150
1	1	3	2	A	162 - 271
2	1	3	2	B	162 - 271
1	1	4	2	A	282 - 330
2	1	4	2	B	282 - 330
1	1	5	2	A	349 - 376
2	1	5	2	B	349 - 376
1	1	6	2	A	400 - 432
2	1	6	2	B	400 - 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)

#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
Sequence details	THERE ARE SEVERAL DISCREPANCES IN SEQUENCE BETWEEN THE DATABASE ANNOTATION AND THE CRYSTALLISED PROTEIN

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44 % Description: HIGH RESOLUTION DATA FROM PDB ENTRY 2XAM WAS NECESARY FOR MODEL COMPLETION AND REFINEMENT
Crystal grow	pH: 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

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9478
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9478 Å / Relative weight: 1
Reflection	Resolution: 3.2→138.69 Å / Num. obs: 15450 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.68 % / B_iso Wilson estimate: 53.8 Å² / R_merge(I) obs: 0.15 / Net I/σ(I): 4.34
Reflection shell	Resolution: 3.2→3.37 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 1.66 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
CCP4		data scaling
SHELX		phasing
autoSHARP		phasing
REFMAC	5.5.0066	refinement

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 3.2→86.71 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c 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.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26835	768	5 %	RANDOM
R_work	0.21049	-	-	-
obs	0.21335	14634	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 21.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	-0 Å²
2-	-	0.52 Å²	0 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→86.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6719	0	132	0	6851

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	6972
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.462	2	9433
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.086	5	838
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.156	24.647	312
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.203	15	1279
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.587	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1049
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5095
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.483	1.5	4203
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.933	2	6789
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.194	3	2769
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.172	4.5	2644
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	164	tight positional	0.04	0.05
1	2	B	164	tight positional	0.04	0.05
2	1	A	364	tight positional	0.05	0.05
2	2	B	364	tight positional	0.05	0.05
3	1	A	440	tight positional	0.05	0.05
3	2	B	440	tight positional	0.05	0.05
4	1	A	196	tight positional	0.04	0.05
4	2	B	196	tight positional	0.04	0.05
5	1	A	112	tight positional	0.05	0.05
5	2	B	112	tight positional	0.05	0.05
6	1	A	132	tight positional	0.04	0.05
6	2	B	132	tight positional	0.04	0.05
1	1	A	152	medium positional	0.05	0.5
1	2	B	152	medium positional	0.05	0.5
2	1	A	366	medium positional	0.07	0.5
2	2	B	366	medium positional	0.07	0.5
3	1	A	424	medium positional	0.06	0.5
3	2	B	424	medium positional	0.06	0.5
4	1	A	196	medium positional	0.06	0.5
4	2	B	196	medium positional	0.06	0.5
5	1	A	105	medium positional	0.06	0.5
5	2	B	105	medium positional	0.06	0.5
6	1	A	161	medium positional	0.07	0.5
6	2	B	161	medium positional	0.07	0.5
1	1	A	164	tight thermal	0.18	0.5
1	2	B	164	tight thermal	0.18	0.5
2	1	A	364	tight thermal	0.28	0.5
2	2	B	364	tight thermal	0.28	0.5
3	1	A	440	tight thermal	0.22	0.5
3	2	B	440	tight thermal	0.22	0.5
4	1	A	196	tight thermal	0.3	0.5
4	2	B	196	tight thermal	0.3	0.5
5	1	A	112	tight thermal	0.28	0.5
5	2	B	112	tight thermal	0.28	0.5
6	1	A	132	tight thermal	0.24	0.5
6	2	B	132	tight thermal	0.24	0.5
1	1	A	152	medium thermal	0.21	2
1	2	B	152	medium thermal	0.21	2
2	1	A	366	medium thermal	0.33	2
2	2	B	366	medium thermal	0.33	2
3	1	A	424	medium thermal	0.25	2
3	2	B	424	medium thermal	0.25	2
4	1	A	196	medium thermal	0.32	2
4	2	B	196	medium thermal	0.32	2
5	1	A	105	medium thermal	0.33	2
5	2	B	105	medium thermal	0.33	2
6	1	A	161	medium thermal	0.26	2
6	2	B	161	medium thermal	0.26	2

LS refinement shell

Resolution: 3.2→3.283 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.309	56	-
R_work	0.265	1072	-
obs	-	-	99.65 %

Refinement TLS params.

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

ID	L11 (°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)
1	2.0893	1.1029	-0.9356	2.0364	-1.602	3.3032	-0.0843	0.1255	-0.1067	-0.2055	0.0416	-0.0573	0.2883	0.1964	0.0427	0.0334	0.0164	-0.0003	0.0384	-0.0115	0.0099	40.3078	69.1124	30.538
2	3.8723	-0.9067	-0.9804	4.0631	0.6603	2.17	-0.2672	-0.0953	0.0226	0.1483	0.2112	-0.0892	0.0712	0.0427	0.0561	0.0486	0.0282	-0.0131	0.0223	-0.0106	0.0077	69.1461	53.4587	79.731
3	0.6837	0.0736	-0.0006	2.0031	-0.5099	0.8313	0.0456	-0.0131	-0.0405	0.0826	0.0088	0.1356	-0.1112	-0.0131	-0.0543	0.0344	-0.0048	0.012	0.0024	-0.0006	0.0155	28.8654	72.7021	48.6354
4	1.1627	0.0122	0.1049	2.2881	-0.0765	0.7664	-0.035	0.1208	0.0667	-0.0588	-0.0633	0.0532	0.0177	-0.1251	0.0983	0.0456	-0.0047	-0.0161	0.1008	-0.0113	0.0215	58.3886	50.4949	60.465

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 150
2	X-RAY DIFFRACTION	2	B	3 - 150
3	X-RAY DIFFRACTION	3	A	160 - 435
4	X-RAY DIFFRACTION	4	B	161 - 435

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi