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- PDB-1w2c: Human Inositol (1,4,5) trisphosphate 3-kinase complexed with Mn2+... -

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Basic information

Entry
Database: PDB / ID: 1w2c
TitleHuman Inositol (1,4,5) trisphosphate 3-kinase complexed with Mn2+/AMPPNP/Ins(1,4,5)P3
ComponentsINOSITOL-TRISPHOSPHATE 3-KINASE A
KeywordsTRANSFERASE / INOSITOL PHOSPHATE KINASE / AMPPNP / IP3
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / inositol metabolic process / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / calmodulin-dependent protein kinase activity / dendritic spine maintenance ...inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / inositol metabolic process / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / calmodulin-dependent protein kinase activity / dendritic spine maintenance / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol phosphate biosynthetic process / cellular response to calcium ion / regulation of synaptic plasticity / small GTPase binding / response to calcium ion / actin cytoskeleton organization / dendritic spine / cytoskeleton / calmodulin binding / phosphorylation / glutamatergic synapse / signal transduction / ATP binding / nucleus / cytosol / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / : / Inositol-trisphosphate 3-kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.95 Å
AuthorsGonzalez, B. / Schell, M.J. / Irvine, R.F. / Williams, R.L.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure of a Human Inositol 1,4,5-Trisphosphate 3-Kinase; Substrate Binding Reveals Why It is not a Phosphoinositide 3-Kinase
Authors: Gonzalez, B. / Schell, M.J. / Letcher, A.J. / Veprintsev, D.B. / Irvine, R.F. / Williams, R.L.
History
DepositionJul 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)63,10211
Polymers60,8512
Non-polymers2,2519
Water5,837324
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A: INOSITOL-TRISPHOSPHATE 3-KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5996
Polymers30,4261
Non-polymers1,1735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: INOSITOL-TRISPHOSPHATE 3-KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5035
Polymers30,4261
Non-polymers1,0774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.063, 97.517, 191.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2048-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.22633, 0.58436, 0.77929), (0.59033, -0.55409, 0.58694), (0.77478, 0.59288, -0.21956)
Vector: -0.8503, 0.08568, 0.29121)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein INOSITOL-TRISPHOSPHATE 3-KINASE A / INOSITOL 1 / 4 / 5-TRISPHOSPHATE 3-KINASE / IP3-3K


Mass: 30425.650 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 197-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P23677, EC: 2.1.7.127

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Non-polymers , 5 types, 333 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O15P3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.6 Å3/Da / Density % sol: 47.3 %
Crystal growpH: 8
Details: 0.835 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH=8, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→55.05 Å / Num. obs: 48847 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 6.68 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.0664
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.91 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.28 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.95→48.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.661 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2329 5 %RANDOM
Rwork0.199 ---
obs0.202 43968 99.6 %-
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: 21.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 127 324 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214365
X-RAY DIFFRACTIONr_bond_other_d0.0020.023961
X-RAY DIFFRACTIONr_angle_refined_deg1.5862.0025899
X-RAY DIFFRACTIONr_angle_other_deg0.96539183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1860.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024726
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02944
X-RAY DIFFRACTIONr_nbd_refined0.2180.2903
X-RAY DIFFRACTIONr_nbd_other0.2490.24600
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.22565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2315
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9231.52547
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6824091
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.37531818
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7834.51808
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 178
Rwork0.245 3401
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)
11.68140.0450.13310.4542-0.16880.98330.0037-0.14960.13180.1284-0.0177-0.1326-0.19650.16470.0140.23950.0135-0.02920.1186-0.02610.145230.73626.09481.352
20.8279-0.0018-0.35970.52730.08930.71750.0110.0411-0.03310.0741-0.03890.0245-0.0069-0.0890.02790.16810.04230.01710.1307-0.00570.15215.39816.56573.209
32.2428-0.0683-1.59160.33120.20951.00920.2813-0.09730.1989-0.0218-0.026-0.089-0.15060.0253-0.25530.19490.05070.12410.1619-0.04680.1211.22527.85389.707
40.97260.451-0.03861.43370.05771.9361-0.0964-0.14310.02390.27520.0683-0.164-0.09450.35550.02810.1680.0354-0.05840.216-0.02590.146810.45259.72477.043
50.39150.0348-0.24320.603-0.23131.1284-0.09460.00740.01570.01730.04360.03020.08250.15320.0510.15640.04240.01210.14120.00340.15171.89751.27361.218
6-0.0168-1.3756-0.15082.29940.70340.7436-0.1343-0.09420.08530.1894-0.0021-0.59770.16090.28120.13630.11920.13070.02650.27520.05540.290422.71246.82855.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A197 - 256
2X-RAY DIFFRACTION2A257 - 268
3X-RAY DIFFRACTION2A324 - 461
4X-RAY DIFFRACTION3A269 - 323
5X-RAY DIFFRACTION4B197 - 256
6X-RAY DIFFRACTION5B257 - 268
7X-RAY DIFFRACTION5B324 - 461
8X-RAY DIFFRACTION6B269 - 323

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