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- PDB-4tz7: Crystal structure of type I phosphatidylinositol 4-phosphate 5-ki... -

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Basic information

Entry
Database: PDB / ID: 4tz7
TitleCrystal structure of type I phosphatidylinositol 4-phosphate 5-kinase alpha from Zebrafish
ComponentsPhosphatidylinositol-4-phosphate 5-kinase, type I, alpha
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


1-phosphatidylinositol-4-phosphate 5-kinase / lipid kinase activity / 1-phosphatidylinositol-4-phosphate 5-kinase activity / phosphatidylinositol phosphate biosynthetic process / phosphorylation / ATP binding / plasma membrane
Similarity search - Function
Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / : / Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. ...Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / : / Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.31 Å
AuthorsHu, J. / Qin, Y. / Wang, J. / Li, L. / Wu, D. / Ha, Y.
CitationJournal: Nat Commun / Year: 2015
Title: Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled.
Authors: Hu, J. / Yuan, Q. / Kang, X. / Qin, Y. / Li, L. / Ha, Y. / Wu, D.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references / Structure summary
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha


Theoretical massNumber of molelcules
Total (without water)44,8691
Polymers44,8691
Non-polymers00
Water0
1
A: Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha

A: Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha


Theoretical massNumber of molelcules
Total (without water)89,7392
Polymers89,7392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area1820 Å2
ΔGint-14 kcal/mol
Surface area29670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.946, 88.946, 157.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha / / Uncharacterized protein


Mass: 44869.309 Da / Num. of mol.: 1 / Fragment: UNP residues 49-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pip5k1aa, pip5k1a / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus RIL / References: UniProt: Q503I3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 20,000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 8877 / % possible obs: 99.5 % / Redundancy: 13.6 % / Net I/σ(I): 30.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 3.31→33.309 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 39.925 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26766 982 10 %RANDOM
Rwork0.20664 ---
obs0.21261 8877 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.849 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20 Å2
2---0.12 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 3.31→33.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 0 0 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192343
X-RAY DIFFRACTIONr_bond_other_d0.0010.022092
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9673174
X-RAY DIFFRACTIONr_angle_other_deg0.82834790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34523.235102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.59215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0671514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02566
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2487.2741208
X-RAY DIFFRACTIONr_mcbond_other4.257.2721207
X-RAY DIFFRACTIONr_mcangle_it6.7810.8981503
X-RAY DIFFRACTIONr_mcangle_other6.77810.8991504
X-RAY DIFFRACTIONr_scbond_it4.9827.6321135
X-RAY DIFFRACTIONr_scbond_other4.9797.6331136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.911.2861671
X-RAY DIFFRACTIONr_long_range_B_refined10.7658.5562639
X-RAY DIFFRACTIONr_long_range_B_other10.76858.5062634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.31→3.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 76 -
Rwork0.254 609 -
obs--96.07 %
Refinement TLS params.Method: refined / Origin x: 14.9591 Å / Origin y: 111.0543 Å / Origin z: 19.1663 Å
111213212223313233
T0.197 Å2-0.2104 Å20.0292 Å2-0.4903 Å2-0.1515 Å2--0.1093 Å2
L5.0059 °2-2.4547 °20.2379 °2-3.0252 °20.7286 °2--3.787 °2
S-0.0216 Å °-1.0528 Å °0.3421 Å °0.4723 Å °0.1137 Å °-0.3245 Å °-0.0169 Å °-0.1481 Å °-0.0922 Å °

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