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- PDB-2q7d: Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinas... -

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Basic information

Entry
Database: PDB / ID: 2q7d
TitleCrystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in complex with AMPPNP and Mn2+
ComponentsInositol-tetrakisphosphate 1-kinase
KeywordsTRANSFERASE / INOSITOL / INOSITOL KINASE / KINASE / ITPK1 / INOSITOL 1 / 3 / 4-5/6-KINASE / PHOSPHATE / INOSITOL PHOSPHATE / INOSITOLPHOSPHATE / POLYPHOSPHATE
Function / homology
Function and homology information


inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development ...inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development / Synthesis of IP3 and IP4 in the cytosol / necroptotic process / catalytic activity / isomerase activity / blood coagulation / Factors involved in megakaryocyte development and platelet production / hydrolase activity / apical plasma membrane / phosphorylation / magnesium ion binding / signal transduction / ATP binding / cytosol
Similarity search - Function
Rossmann fold - #11370 / Inositol-tetrakisphosphate 1-kinase, N-terminal / Inositol 1,3,4-trisphosphate 5/6-kinase pre-ATP-grasp domain / Inositol-tetrakisphosphate 1-kinase / Inositol 1,3,4-trisphosphate 5/6-kinase, ATP-grasp domain / Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 ...Rossmann fold - #11370 / Inositol-tetrakisphosphate 1-kinase, N-terminal / Inositol 1,3,4-trisphosphate 5/6-kinase pre-ATP-grasp domain / Inositol-tetrakisphosphate 1-kinase / Inositol 1,3,4-trisphosphate 5/6-kinase, ATP-grasp domain / Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Inositol-tetrakisphosphate 1-kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChamberlain, P.P. / Lesley, S.A. / Spraggon, G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Integration of inositol phosphate signaling pathways via human ITPK1.
Authors: Chamberlain, P.P. / Qian, X. / Stiles, A.R. / Cho, J. / Jones, D.H. / Lesley, S.A. / Grabau, E.A. / Shears, S.B. / Spraggon, G.
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 21, 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_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol-tetrakisphosphate 1-kinase
B: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,44820
Polymers78,0632
Non-polymers2,38518
Water12,773709
1
A: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,32011
Polymers39,0311
Non-polymers1,28910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1289
Polymers39,0311
Non-polymers1,0968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-227 kcal/mol
Surface area29700 Å2
MethodPISA, PQS
4
A: Inositol-tetrakisphosphate 1-kinase
hetero molecules

B: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,44820
Polymers78,0632
Non-polymers2,38518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area5700 Å2
ΔGint-213 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.157, 94.607, 130.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMONOMER ESTABLISHED BY SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING

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Components

#1: Protein Inositol-tetrakisphosphate 1-kinase / / Inositol- triphosphate 5/6-kinase / Inositol 1 / 3 / 4-trisphosphate 5/6-kinase / Ins1 / 3 / 4 / P3 ...Inositol- triphosphate 5/6-kinase / Inositol 1 / 3 / 4-trisphosphate 5/6-kinase / Ins1 / 3 / 4 / P3 / 5/6-kinase


Mass: 39031.348 Da / Num. of mol.: 2 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITPK1 / Plasmid: MH4 / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q13572, inositol-tetrakisphosphate 1-kinase, inositol-1,3,4-trisphosphate 5/6-kinase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Na Citrate, 0.2M K/Na Tartrate, 2M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 95421 / Num. obs: 95421 / % possible obs: 91.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.1
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Selenomethionine derivative partially refined structure

Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.279 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23594 4790 5 %RANDOM
Rwork0.19383 ---
obs0.19593 90414 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.038 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---0.33 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 126 709 6198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225695
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9797755
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37224.338272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.089151003
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3671536
X-RAY DIFFRACTIONr_chiral_restr0.10.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024246
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23027
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23962
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2688
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.37943486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.25165571
X-RAY DIFFRACTIONr_scbond_it3.44852397
X-RAY DIFFRACTIONr_scangle_it5.04782164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 326 -
Rwork0.264 6589 -
obs--91.53 %
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)
10.1755-0.02470.00850.6426-0.00060.99090.0083-0.00260.0033-0.01750.027-0.02270.03170.002-0.0353-0.05870.0082-0.0042-0.0339-0.0026-0.0243-5.541619.7688-31.9641
20.44390.13630.10110.47570.27120.84230.024-0.0210.0148-0.0187-0.0230.0621-0.0372-0.0737-0.0009-0.03870.01470.0174-0.04310.0022-0.0191-26.267845.6862-12.9513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-7 - 3304 - 341
2X-RAY DIFFRACTION2BB-3 - 3308 - 341

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