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- PDB-1tzd: CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF INOSITOL 1,4,5-TRISPHO... -

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Basic information

Entry
Database: PDB / ID: 1tzd
TitleCRYSTAL STRUCTURE OF THE CATALYTIC CORE OF INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE
ComponentsInositol-trisphosphate 3-kinase A
KeywordsTRANSFERASE / INOSITOL KINASE
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / inositol-trisphosphate 3-kinase / Synthesis of IP3 and IP4 in the cytosol / inositol hexakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate biosynthetic process / inositol metabolic process / positive regulation of dendritic spine morphogenesis / dendritic spine maintenance / calcium/calmodulin-dependent protein kinase activity ...small GTPase binding => GO:0031267 / inositol-trisphosphate 3-kinase / Synthesis of IP3 and IP4 in the cytosol / inositol hexakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate biosynthetic process / inositol metabolic process / positive regulation of dendritic spine morphogenesis / dendritic spine maintenance / calcium/calmodulin-dependent protein kinase activity / phosphatidylinositol phosphate biosynthetic process / regulation of synaptic plasticity / kinase activity / actin cytoskeleton organization / dendritic spine / calmodulin binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / D-amino Acid Aminotransferase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Inositol-trisphosphate 3-kinase A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.2 Å
AuthorsMiller, G.J. / Hurley, J.H.
CitationJournal: Mol.Cell / Year: 2004
Title: Crystal structure of the catalytic core of inositol 1,4,5-trisphosphate 3-kinase
Authors: Miller, G.J. / Hurley, J.H.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jun 19, 2013Group: Refinement description
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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-trisphosphate 3-kinase A
B: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4615
Polymers63,5822
Non-polymers8793
Water6,792377
1
A: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2433
Polymers31,7911
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2182
Polymers31,7911
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.679, 98.535, 188.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Inositol-trisphosphate 3-kinase A / Inositol 1 / 4 / 5-trisphosphate 3-kinase A / IP3K A / IP3 3-kinase A


Mass: 31791.094 Da / Num. of mol.: 2 / Fragment: catalytic core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Itpka / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3)
References: UniProt: P17105, inositol-trisphosphate 3-kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2.2M AMMONIUM sulfate, 0.2M SODIUM FORMATE, 10 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 32563

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→38.92 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.827 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3052 1640 5 %RANDOM
Rwork0.25748 ---
obs0.25992 30923 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---2.26 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 55 377 4345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9865245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9563475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.84415702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022915
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.4290.33237
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4950.5670
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3840.377
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.52362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26223767
X-RAY DIFFRACTIONr_scbond_it2.12131522
X-RAY DIFFRACTIONr_scangle_it3.1944.51471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 94
Rwork0.251 2255
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)
13.3174-1.003-0.74113.3731-2.33615.4459-0.1836-0.710.66491.25880.1236-0.3044-1.280.57510.060.59640.1492-0.07340.4765-0.07390.276429.97925.339-13.593
24.0185-0.4233-2.5292.82830.08884.4689-0.1785-0.1025-0.09240.41480.1350.4465-0.0021-0.30180.04350.13560.12770.09780.19080.03780.16815.14218.784-22.241
316.0779-1.3083-17.58765.6295-1.036610.33110.6496-2.62190.98551.8223-0.8607-0.12020.1041.2480.21110.67580.00130.16290.8482-0.03070.32257.17921.2380.696
411.45042.13382.15527.44742.68338.1540.95380.16730.305-0.1244-0.3999-0.8072-0.095-0.6788-0.55390.56060.20690.20280.66380.16290.5168-3.47133.521-6.646
5-4.1156-4.1842.80315.10966.818217.21710.0032-0.0268-0.35230.3531-0.0166-0.4705-0.6156-0.42370.01350.33770.14140.16970.55770.04270.44851.77725.646-12.024
62.60081.0041-1.34267.09810.34763.1368-0.2717-0.9892-0.35371.18990.1821-1.0957-0.08311.15140.08960.39820.2032-0.14030.6802-0.0070.2729.46462.456-18.564
73.0215-0.6494-1.95192.2105-0.46194.356-0.399-0.2284-0.4250.2890.17360.00220.37420.31370.22540.15370.15070.07220.17890.01860.12112.2952.617-33.272
816.9527-4.15452.563511.54781.7434-2.4962-1.25330.71610.58010.32860.3259-2.251-0.5031.46810.92730.31060.05510.03910.74630.17370.604524.59159.464-42.211
94.58755.0506-1.61158.7721-1.91465.2134-0.4999-0.1095-1.0441-0.256-0.2122-2.2670.19260.96480.71210.64020.15360.12330.97240.24971.07526.47941.645-43.284
1040.222428.1249-3.756319.74055.0243-0.9321-0.0696-1.1488-1.44830.0244-0.4333-2.85760.31550.16150.50290.41380.32710.17720.49150.17150.784917.79847.392-41.991
110.0227-0.69960.2990.9982-0.5021-0.132-0.1058-0.1486-0.00740.25730.0989-0.0693-0.04260.02620.00690.48430.04940.08980.5721-0.00980.41311.43638.025-25.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A203 - 254
2X-RAY DIFFRACTION2A255 - 267
3X-RAY DIFFRACTION2A322 - 457
4X-RAY DIFFRACTION2A1 - 2
5X-RAY DIFFRACTION3A268 - 278
6X-RAY DIFFRACTION4A279 - 304
7X-RAY DIFFRACTION5A311 - 321
8X-RAY DIFFRACTION6B203 - 254
9X-RAY DIFFRACTION7B255 - 267
10X-RAY DIFFRACTION7B322 - 457
11X-RAY DIFFRACTION7B1
12X-RAY DIFFRACTION8B268 - 278
13X-RAY DIFFRACTION9B279 - 304
14X-RAY DIFFRACTION10B311 - 321
15X-RAY DIFFRACTION11A460 - 639
16X-RAY DIFFRACTION11B460 - 656

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