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- PDB-2aqx: Crystal Structure of the Catalytic and CaM-Binding domains of Ino... -

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Basic information

Entry
Database: PDB / ID: 2aqx
TitleCrystal Structure of the Catalytic and CaM-Binding domains of Inositol 1,4,5-Trisphosphate 3-Kinase B
ComponentsPREDICTED: inositol 1,4,5-trisphosphate 3-kinase B
KeywordsTRANSFERASE / IP3K / ITPKB / IP3-3K / IP3-3KB / inositol / kinase / IP3 / Calmodulin binding
Function / homology
Function and homology information


negative regulation of neutrophil apoptotic process / thymic T cell selection / inositol-trisphosphate 3-kinase / Synthesis of IP3 and IP4 in the cytosol / Synthesis of IP3 and IP4 in the cytosol / inositol trisphosphate metabolic process / inositol hexakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / Transferases; Transferring phosphorus-containing groups / inositol phosphate biosynthetic process ...negative regulation of neutrophil apoptotic process / thymic T cell selection / inositol-trisphosphate 3-kinase / Synthesis of IP3 and IP4 in the cytosol / Synthesis of IP3 and IP4 in the cytosol / inositol trisphosphate metabolic process / inositol hexakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / Transferases; Transferring phosphorus-containing groups / inositol phosphate biosynthetic process / negative regulation of myeloid cell differentiation / common myeloid progenitor cell proliferation / positive thymic T cell selection / positive regulation of Ras protein signal transduction / positive regulation of alpha-beta T cell differentiation / myeloid cell homeostasis / phosphatidylinositol phosphate biosynthetic process / T cell differentiation / cellular response to calcium ion / regulation of protein phosphorylation / MAPK cascade / kinase activity / cell surface receptor signaling pathway / calmodulin binding / ATP binding / membrane / nucleus / cytoplasm / cytosol
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'-TRIPHOSPHATE / Kinase / Inositol-trisphosphate 3-kinase B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChamberlain, P.P. / Sandberg, M.L. / Sauer, K. / Cooke, M.P. / Lesley, S.A. / Spraggon, G.
CitationJournal: Biochemistry / Year: 2005
Title: Structural insights into enzyme regulation for inositol 1,4,5-trisphosphate 3-kinase B
Authors: Chamberlain, P.P. / Sandberg, M.L. / Sauer, K. / Cooke, M.P. / Lesley, S.A. / Spraggon, G.
History
DepositionAug 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_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: PREDICTED: inositol 1,4,5-trisphosphate 3-kinase B
B: PREDICTED: inositol 1,4,5-trisphosphate 3-kinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9748
Polymers66,8632
Non-polymers1,1126
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-68 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.204, 60.655, 56.851
Angle α, β, γ (deg.)59.90, 72.74, 88.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PREDICTED: inositol 1,4,5-trisphosphate 3-kinase B


Mass: 33431.312 Da / Num. of mol.: 2 / Fragment: CaM-binding domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: P42335, UniProt: B2RXC2*PLUS, inositol-trisphosphate 3-kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.1 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350, Magnesium Chloride, HEPES, ATP, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2004
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 20323 / Num. obs: 19368 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 83.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.88 / SU B: 17.62 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 979 5.1 %RANDOM
Rwork0.18447 ---
all0.18923 19368 --
obs0.18876 18227 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.853 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-1.16 Å21.53 Å2
2---0.28 Å21.8 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 66 99 4837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9786511
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0665573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41423.966232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08415908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9661538
X-RAY DIFFRACTIONr_chiral_restr0.1280.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023610
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.22397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23244
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.721.52958
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23724630
X-RAY DIFFRACTIONr_scbond_it1.79932146
X-RAY DIFFRACTIONr_scangle_it2.9364.51881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 61 -
Rwork0.234 1172 -
obs--82.42 %
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)
10.53320.16070.37490.6220.23681.3520.0448-0.0477-0.02890.0099-0.06150.11820.1219-0.1170.0167-0.0209-0.00650.0143-0.02870.0006-0.0172-9.65341.547125.382
21.2439-0.44720.77310.8032-0.63011.21730.0114-0.06580.1349-0.0389-0.1173-0.14760.011-0.01780.1059-0.01370.01180.0045-0.02880.0213-0.006327.356447.452951.8884
32.0029-1.5432-1.17433.871-0.741610.23160.0658-0.06420.3986-0.3383-0.2903-0.3349-0.3013-0.03570.2245-0.05930.0236-0.0312-0.09460.0123-0.1067-14.535440.2411-2.7823
41.30070.9463-1.60820.85640.322315.25490.3504-0.4755-0.13950.5745-1.00450.05150.0340.63840.6540.2091-0.1512-0.08970.24740.0776-0.030235.427736.638681.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA651 - 7592 - 110
2X-RAY DIFFRACTION1AA803 - 937154 - 288
3X-RAY DIFFRACTION2BB651 - 7592 - 110
4X-RAY DIFFRACTION2BB803 - 937154 - 288
5X-RAY DIFFRACTION3AA760 - 802111 - 153
6X-RAY DIFFRACTION4BB760 - 802111 - 153

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