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- PDB-5e3t: Crystal structure of phosphatidylinositol-4-phosphate 5-kinase -

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Basic information

Entry
Database: PDB / ID: 5e3t
TitleCrystal structure of phosphatidylinositol-4-phosphate 5-kinase
ComponentsPhosphatidylinositol-4-phosphate 5-kinase, type I, alpha
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


Synthesis of PIPs at the plasma membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 1-phosphatidylinositol-4-phosphate 5-kinase / lipid kinase activity / 1-phosphatidylinositol-4-phosphate 5-kinase activity / phosphatidylinositol phosphate biosynthetic process / phosphorylation / ATP binding / metal ion 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsMuftuoglu, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mechanism of substrate specificity of phosphatidylinositol phosphate kinases.
Authors: Muftuoglu, Y. / Xue, Y. / Gao, X. / Wu, D. / Ha, Y.
History
DepositionOct 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8714
Polymers42,2551
Non-polymers6163
Water543
1
A: Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)85,7438
Polymers84,5112
Non-polymers1,2326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area4050 Å2
ΔGint-47 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.928, 87.928, 156.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 42255.422 Da / Num. of mol.: 1 / Fragment: unp residues 56-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pip5k1aa, pip5k1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q503I3
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.58 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: peg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. all: 9831 / Num. obs: 9831 / % possible obs: 99.5 % / Redundancy: 9.3 % / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
Cootmodel building
RefinementResolution: 3.3→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 21.993 / SU ML: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.063 / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 470 4.8 %RANDOM
Rwork0.204 ---
obs0.2074 9331 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 184.59 Å2 / Biso mean: 96.349 Å2 / Biso min: 57.62 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å2-0 Å2-0 Å2
2--3.26 Å2-0 Å2
3----6.51 Å2
Refinement stepCycle: final / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 33 3 2304
Biso mean--96.72 80.49 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192353
X-RAY DIFFRACTIONr_bond_other_d0.0020.022088
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9743199
X-RAY DIFFRACTIONr_angle_other_deg0.89734762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7875298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10323.0399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2581514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_mcbond_it7.34710.2391204
X-RAY DIFFRACTIONr_mcbond_other7.34310.2371203
X-RAY DIFFRACTIONr_mcangle_it11.36215.3161498
LS refinement shellResolution: 3.294→3.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 35 -
Rwork0.316 679 -
all-714 -
obs--99.03 %

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