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- PDB-1z2n: Inositol 1,3,4-trisphosphate 5/6-kinase complexed Mg2+/ADP -

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Basic information

Entry
Database: PDB / ID: 1z2n
TitleInositol 1,3,4-trisphosphate 5/6-kinase complexed Mg2+/ADP
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 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 / phosphorylation / 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 / Inositol-tetrakisphosphate 1-kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 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 / 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 / _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)37,3883
Polymers36,9361
Non-polymers4522
Water9,944552
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.359, 94.267, 47.276
Angle α, β, γ (deg.)90.00, 110.26, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Plasmid: pGEX-3T / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 278 K / pH: 5.5
Details: 25% PEG 3350, 0.1 M bis-tris, 10 mM DTT, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 5.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
31
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211
SYNCHROTRONNSLS X2520.9687,1.0095,1.007,1.008
SYNCHROTRONALS 8.2.131.8997,1.8453
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 3152CCD
ADSC QUANTUM 2103CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.96871
31.00951
41.0071
51.0081
61.89971
71.84531
ReflectionResolution: 1.2→47 Å / Num. all: 91950 / Num. obs: 91950 / % possible obs: 99 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 99.4 % / Rmerge(I) obs: 0.246

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.2→47 Å / SU B: 0.722 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4408 5 %RANDOM
Rwork0.182 ---
obs0.182 83625 99.1 %-
Displacement parametersBiso mean: 17.42 Å2 / Baniso 11: -0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.2→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 28 552 3084
LS refinement shellResolution: 1.2→1.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 321 -
Rwork0.213 6200 -
obs--99.5 %

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