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- PDB-1z2o: Inositol 1,3,4-trisphosphate 5/6-Kinase in complex with mg2+/ADP/... -

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Basic information

Entry
Database: PDB / ID: 1z2o
TitleInositol 1,3,4-trisphosphate 5/6-Kinase in complex with mg2+/ADP/Ins(1,3,4,6)P4
Componentsinositol 1,3,4-trisphosphate 5/6-kinase
KeywordsTRANSFERASE / Inositol phosphate kinase / ATP-grasp
Function / homology
Function and homology information


inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol trisphosphate metabolic process / isomerase activity / magnesium ion binding / ATP binding
Similarity search - Function
Dna Ligase; domain 1 - #220 / Inositol 1,3,4-trisphosphate 5/6-kinase domain / : / Inositol-tetrakisphosphate 1-kinase, preATP-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. ...Dna Ligase; domain 1 - #220 / Inositol 1,3,4-trisphosphate 5/6-kinase domain / : / Inositol-tetrakisphosphate 1-kinase, preATP-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 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / (1S,3R,4R,6S)-1,3,4,6-TETRAPKISPHOSPHATE / Inositol-tetrakisphosphate 1-kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.24 Å
AuthorsMiller, G.J. / Wilson, M.P. / Majerus, P.W. / Hurley, J.H.
CitationJournal: Mol.Cell / Year: 2005
Title: Specificity determinants in inositol polyphosphate synthesis: crystal structure of inositol 1,3,4-trisphosphate 5/6-kinase.
Authors: Miller, G.J. / Wilson, M.P. / Majerus, P.W. / Hurley, J.H.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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

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Assembly

Deposited unit
X: inositol 1,3,4-trisphosphate 5/6-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9125
Polymers36,9361
Non-polymers9764
Water9,692538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.189, 94.294, 47.351
Angle α, β, γ (deg.)90.00, 110.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein inositol 1,3,4-trisphosphate 5/6-kinase


Mass: 36936.441 Da / Num. of mol.: 1 / Fragment: Inositol phosphate kinase, ATP-grasp
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Plasmid: PGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q9XYQ1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-I4P / (1S,3R,4R,6S)-1,3,4,6-TETRAPKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.1 M bis-tris, 10 mM DTT, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
1,2,31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 86579 / % possible obs: 98.6 %
Reflection shellResolution: 1.24→1.28 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.24→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.208 -RANDOM
Rwork0.189 --
obs-86579 -
Refinement stepCycle: LAST / Resolution: 1.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 57 538 3099

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