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

ID or keywords:

Entry

Database: PDB / ID: 2xao

Title

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP5

Components

INOSITOL-PENTAKISPHOSPHATE 2-KINASE

Keywords

TRANSFERASE /

INOSITOL POLYPHOSPHATE KINASE / 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 ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 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 / Refinement description / Version format compliance
Revision 1.2	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 1.3	Dec 20, 2023	Group: 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_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_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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2xao.cif.gz	174.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2xao.ent.gz	139.1 KB	Display	PDB format
PDBx/mmJSON format	2xao.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xa/2xao ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xao	HTTPS FTP

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Related structure data

Related structure data	2xalC 2xamSC 2xanC 2xarC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xar-1 4ucn-d 4c0b-2 4lv7-2 4lv7-1 6ung-d 3udz-3 6fyk-1 2r4e-2 3b98-2 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

Deposited unit

A: INOSITOL-PENTAKISPHOSPHATE 2-KINASE

B: INOSITOL-PENTAKISPHOSPHATE 2-KINASE

hetero molecules

103 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
51.4 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
51.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.761, 112.737, 144.454
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:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	ARG	ARG	A	A	5 - 45	5 - 45
2	1	LEU	LEU	ARG	ARG	B	B	5 - 45	5 - 45
1	2	VAL	VAL	SER	SER	A	A	60 - 150	60 - 150
2	2	VAL	VAL	SER	SER	B	B	60 - 150	60 - 150
1	3	CYS	CYS	ALA	ALA	A	A	162 - 271	162 - 271
2	3	CYS	CYS	ALA	ALA	B	B	162 - 271	162 - 271
1	4	HIS	HIS	CYS	CYS	A	A	282 - 330	282 - 330
2	4	HIS	HIS	CYS	CYS	B	B	282 - 330	282 - 330
1	5	PRO	PRO	GLN	GLN	A	A	349 - 376	349 - 376
2	5	PRO	PRO	GLN	GLN	B	B	349 - 376	349 - 376
1	6	ASP	ASP	ARG	ARG	A	A	400 - 432	400 - 432
2	6	ASP	ASP	ARG	ARG	B	B	400 - 432	400 - 432

NCS ensembles :

ID
1
2
3
4
5
6

NCS oper: (Code: given
Matrix: (0.99878, 0.02197, 0.04431), (0.02544, -0.99652, -0.07934), (0.04241, 0.08037, -0.99586)
Vector: -33.12381, 128.42226, 107.56577)

#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-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-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence details	THERE ARE SEVERAL DISCREPANCIES IN SEQUENCE BETWEEN THE UNIPROT DATABASE ANNOTATION AND THE ...THERE ARE SEVERAL DISCREPANCIES IN SEQUENCE BETWEEN THE UNIPROT 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: 2.3 Å³/Da / Density % sol: 47.7 % / Description: NONE
Crystal grow	pH: 5.9 Details: 22% PEG 3300, 100 MM BIS-TRIS PH 5.9, 2 MM MGCL2. PROTEIN WAS MIXED WITH 2 MM INOSITOL-5-P

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Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9538
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9538 Å / Relative weight: 1
Reflection	Resolution: 2.7→88.74 Å / Num. obs: 22033 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.92 % / B_iso Wilson estimate: 57 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 4.24
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 6.99 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 1.66 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
CCP4		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XAM

2xam

Resolution: 2.9→88.736 Å / Cor.coef. F_o:F_c: 0.9 / Cor.coef. F_o:F_c free: 0.825 / SU B: 39.372 / SU ML: 0.364 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2907	1141	5.21 %	RANDOM
R_work	0.2249	-	-	-
obs	0.228	21980	99.995 %	-

Solvent computation

Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 38.993 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.267 Å²	0 Å²	0 Å²
2-	-	-1.716 Å²	0 Å²
3-	-	-	1.449 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→88.736 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6602	0	66	0	6668

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	6785
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.371	1.989	9162
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.543	5	819
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.168	24.56	307
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.117	15	1259
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.598	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1024
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4973
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	2930
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	4636
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	169
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.063	0.2	2
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.215	0.2	46
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.086	0.2	2
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	0.524	1.5	4219
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.937	2	6651
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.067	3	2855
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.847	4.5	2511
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
2	1	A	364	tight positional	0.04	0.05
3	1	A	432	tight positional	0.04	0.05
4	1	A	196	tight positional	0.04	0.05
5	1	A	112	tight positional	0.05	0.05
6	1	A	132	tight positional	0.04	0.05
1	2	B	152	medium positional	0.47	0.5
2	2	B	366	medium positional	0.55	0.5
3	2	B	422	medium positional	0.5	0.5
4	2	B	196	medium positional	0.39	0.5
5	2	B	105	medium positional	0.43	0.5
6	2	B	161	medium positional	0.46	0.5
1	1	A	164	tight thermal	0.14	0.5
2	1	A	364	tight thermal	0.17	0.5
3	1	A	432	tight thermal	0.14	0.5
4	1	A	196	tight thermal	0.2	0.5
5	1	A	112	tight thermal	0.18	0.5
6	1	A	132	tight thermal	2.36	0.5
1	2	B	152	medium thermal	0.32	2
2	2	B	366	medium thermal	0.35	2
3	2	B	422	medium thermal	0.44	2
4	2	B	196	medium thermal	0.45	2
5	2	B	105	medium thermal	0.55	2
6	2	B	161	medium thermal	1.67	2

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	72	-
R_work	0.297	1513	-
obs	-	-	100 %

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	1.5072	0.6936	-0.9456	2.102	-0.5296	1.5122	-0.0819	-0.0349	-0.0781	-0.5004	0.0835	-0.2489	0.0989	0.0114	-0.0015	0.1245	0.0136	0.0548	-0.0345	0.0072	-0.1177	42.738	70.4271	32.5716
2	1.9289	-0.3562	0.2957	1.6207	-0.3095	2.3563	-0.0775	-0.0222	-0.0162	0.3339	0.0573	-0.1521	-0.1083	0.2215	0.0202	-0.1151	-0.0022	-0.0515	-0.0689	-0.0296	-0.1158	71.4538	54.01	82.5276
3	0.5829	-0.2201	-0.092	2.8399	-0.6069	0.9778	0.0256	0.0066	-0.0108	-0.0344	-0.0312	0.0579	-0.0811	-0.0411	0.0056	-0.0598	-0.004	-0.0032	-0.0705	0.0211	-0.1071	31.5006	73.7452	51.4594
4	1.0149	0.2788	-0.2118	3.3424	-0.0451	0.5898	-0.0197	0.0921	0.0609	-0.1311	-0.0164	0.1707	-0.0115	-0.0497	0.0361	-0.1415	0.0275	-0.075	-0.0402	0.0031	-0.0525	60.5289	51.3214	63.481
5	7.9154	-30.2495	-6.5862	118.8141	31.733	18.8909	0.4671	0.3268	0.2792	-2.0779	-2.069	-0.6677	1.5484	-2.2294	1.602	0.004	0.0042	0.0011	0.0017	-0.0001	-0.0007	28.5382	87.9851	30.667
6	486.8928	240.4668	9.9803	263.1732	68.1124	27.8487	2.5272	-3.6034	-1.6329	7.3634	-2.4258	2.3978	-1.3002	0.7187	-0.1014	0.0103	-0.0021	0.0136	0.0014	0.0203	0.0131	57.9037	35.801	82.3946

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	161 - 435
4	X-RAY DIFFRACTION	4	B	161 - 435
5	X-RAY DIFFRACTION	5	A	151 - 160
6	X-RAY DIFFRACTION	6	B	151 - 153

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