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- PDB-2a98: Crystal structure of the catalytic domain of human inositol 1,4,5... -

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Basic information

Entry
Database: PDB / ID: 2a98
TitleCrystal structure of the catalytic domain of human inositol 1,4,5-trisphosphate 3-kinase C
ComponentsInositol 1,4,5-trisphosphate 3-kinase C
KeywordsTRANSFERASE / kinase / inositol / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / inositol hexakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol phosphate biosynthetic process / kinase activity / calmodulin binding / nuclear speck ...inositol-trisphosphate 3-kinase / inositol hexakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol phosphate biosynthetic process / kinase activity / calmodulin binding / nuclear speck / ATP binding / 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
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol-trisphosphate 3-kinase C / Inositol-trisphosphate 3-kinase C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHallberg, B.M. / Ogg, D. / Ehn, M. / Graslund, S. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Persson, C. / Sagemark, J. ...Hallberg, B.M. / Ogg, D. / Ehn, M. / Graslund, S. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Persson, C. / Sagemark, J. / Schuler, H. / Stenmark, P. / Thorsell, A.-G. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of the catalytic domain of human inositol 1,4,5-trisphosphate 3-kinase C
Authors: Hallberg, B.M. / Ogg, D. / Arrowsmith, C. / Edwards, A. / Ehn, M. / Graslund, S. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Persson, C. / Sagemark, J. / Schuler, H. ...Authors: Hallberg, B.M. / Ogg, D. / Arrowsmith, C. / Edwards, A. / Ehn, M. / Graslund, S. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Persson, C. / Sagemark, J. / Schuler, H. / Stenmark, P. / Thorsell, A.-G. / Sundstrom, M. / Weigelt, J.
History
DepositionJul 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1,4,5-trisphosphate 3-kinase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0652
Polymers29,6451
Non-polymers4201
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.720, 87.720, 174.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Inositol 1,4,5-trisphosphate 3-kinase C


Mass: 29644.883 Da / Num. of mol.: 1 / Fragment: Kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta-2
References: UniProt: Q9Y475, UniProt: Q96DU7*PLUS, inositol-trisphosphate 3-kinase
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG3350, Sodium thiocyanate, Magnesium chloride, inositol 1,4,5-trisphosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 28, 2005
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→28.68 Å / Num. all: 12906 / Num. obs: 12906 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.79
Reflection shellResolution: 2.6→2.65 Å / % possible obs: 86.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 3.7 / Num. measured obs: 11858 / Num. unique obs: 1335 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1w2c

1w2c


Resolution: 2.6→28.68 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 21.235 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.426 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 629 4.9 %RANDOM
Rwork0.218 ---
all0.22 13501 --
obs0.22 12872 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.726 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å20 Å2
2--0.29 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 24 0 2099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222144
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9822901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8645258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67624.272103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.94115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7011515
X-RAY DIFFRACTIONr_chiral_restr0.1790.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021614
X-RAY DIFFRACTIONr_nbd_refined0.2410.2814
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.22
X-RAY DIFFRACTIONr_mcbond_it0.5741.51327
X-RAY DIFFRACTIONr_mcangle_it0.95622080
X-RAY DIFFRACTIONr_scbond_it1.6823919
X-RAY DIFFRACTIONr_scangle_it2.4884.5821
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 61 -
Rwork0.293 867 -
all-928 -
obs--100 %
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)
111.80281.8293-0.793740.1306-6.375714.0423-0.3586-1.13550.52060.64950.5520.9279-1.4592-0.1921-0.1934-0.05130.06180.02770.452-0.06610.098313.12246.0930.045
29.488-1.80310.62566.4154-5.376518.92880.2281.02490.0106-0.7929-0.4439-0.53280.77271.39140.2160.14050.04470.13780.22110.05080.15248.12337.638-10.693
311.4523-2.0195-0.98720.9309-0.05770.1785-0.6232-0.21171.06270.34630.6728-0.3475-0.38360.1524-0.04960.19060.0055-0.06380.2078-0.01320.319510.09848.898-1.743
40.42761.0937-0.336410.7773-3.39913.808-0.02840.4472-0.24910.4274-0.6214-0.74840.72390.53950.64980.13290.09690.07030.04450.06730.2214-2.01332.1122.975
58.3186-1.38390.51638.77241.09949.397-0.2356-0.663-0.93360.84550.2429-0.74031.99741.4943-0.00720.55890.35540.03230.33720.21510.61282.70624.06817.827
61.9943-1.6866-0.0475.72132.14939.429-0.2886-0.1877-0.24480.12620.05460.05450.0706-0.32240.2339-0.0560.05060.0211-0.00840.06330.1618-12.12838.9537.924
711.8432-8.4523-2.25112.78252.78356.41380.3930.9971-0.3499-1.385-0.71690.6017-0.1992-0.53640.32390.1245-0.06290.00160.08680.07230.0922-8.61238.856-10.415
85.4068-0.5305-0.40457.94841.71114.1089-0.16070.4904-0.5318-0.5193-0.0117-0.62540.74830.23080.17240.14560.0340.15170.09420.04160.1023-0.32831.879-4.799
96.2945-6.9182-1.92648.4988-0.02869.8140.1243-0.0019-0.6594-0.49530.12710.6380.0271-0.517-0.25140.0865-0.10170.03590.0773-0.00230.1983-14.90734.127-4.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A425 - 435
2X-RAY DIFFRACTION2A436 - 453
3X-RAY DIFFRACTION3A454 - 480
4X-RAY DIFFRACTION4A481 - 494
5X-RAY DIFFRACTION5A495 - 543
6X-RAY DIFFRACTION6A544 - 585
7X-RAY DIFFRACTION7A586 - 614
8X-RAY DIFFRACTION8A615 - 664
9X-RAY DIFFRACTION9A665 - 683

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