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- PDB-6cn3: Crystal structure of zebrafish Phosphatidylinositol-4-phosphate 5... -

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Basic information

Entry
Database: PDB / ID: 6cn3
TitleCrystal structure of zebrafish Phosphatidylinositol-4-phosphate 5- kinase alpha isoform D236A
ComponentsPhosphatidylinositol-4-phosphate 5-kinase, type I, alpha
KeywordsTRANSFERASE / PIP5Ka / ATP / D236A
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 / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / 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 Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / 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 I, alpha
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.351 Å
AuthorsZeng, X. / Sui, D. / Hu, J.
CitationJournal: Biochem. J. / Year: 2018
Title: Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5K gamma.
Authors: Zeng, X. / Uyar, A. / Sui, D. / Donyapour, N. / Wu, D. / Dickson, A. / Hu, J.
History
DepositionMar 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,8251
Polymers44,8251
Non-polymers00
Water00
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)89,6512
Polymers89,6512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1850 Å2
ΔGint-14 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.327, 89.327, 156.655
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 / Phosphatidylinositol-4-phosphate 5-kinase / type I / alpha / a


Mass: 44825.297 Da / Num. of mol.: 1 / Mutation: C-terminal fusion to HHHHHH, D236A
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

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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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mg/ml protein, mixed with 0.1 M MES pH 6.5, 12% PEG 20000.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.35→40 Å / Num. obs: 9691 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 101.32 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.032 / Rrim(I) all: 0.119 / Χ2: 0.816 / Net I/σ(I): 6 / Num. measured all: 135819
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.35-3.4714.30.8489360.8980.2310.8790.626100
3.47-3.6114.30.5379430.9540.1460.5570.614100
3.61-3.7714.30.349350.9770.0930.3530.651100
3.77-3.9714.40.2419480.9890.0650.250.684100
3.97-4.2214.40.1869560.9930.050.1930.776100
4.22-4.5514.30.1459510.9950.040.1510.935100
4.55-514.20.1229680.9950.0330.1270.915100
5-5.7214.10.1129710.9970.0310.1160.95100
5.72-7.213.80.0839980.9980.0230.0861.039100
7.2-4012.40.04910850.9990.0150.0520.96299.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZ7

4tz7


Resolution: 3.351→39.948 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.29
RfactorNum. reflection% reflection
Rfree0.2717 493 5.11 %
Rwork0.2302 --
obs0.2324 9645 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.45 Å2 / Biso mean: 94.8995 Å2 / Biso min: 30.02 Å2
Refinement stepCycle: final / Resolution: 3.351→39.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 0 0 2305
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012361
X-RAY DIFFRACTIONf_angle_d1.2273198
X-RAY DIFFRACTIONf_chiral_restr0.064353
X-RAY DIFFRACTIONf_plane_restr0.008414
X-RAY DIFFRACTIONf_dihedral_angle_d3.4731399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.351-3.68810.33071150.268822242339
3.6881-4.22120.27581170.228822582375
4.2212-5.31630.27821210.221822712392
5.3163-39.95110.25451400.22623992539

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