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- PDB-6cn2: Crystal structure of zebrafish Phosphatidylinositol-4-phosphate 5... -

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Basic information

Entry
Database: PDB / ID: 6cn2
TitleCrystal structure of zebrafish Phosphatidylinositol-4-phosphate 5- kinase alpha isoform D236N with bound ATP/Ca2+
ComponentsPhosphatidylinositol-4-phosphate 5-kinase, type I, alpha
KeywordsTRANSFERASE / PIP5Ka / ATP / D236N
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
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
ADENOSINE-5'-TRIPHOSPHATE / Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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)45,4564
Polymers44,8681
Non-polymers5873
Water181
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)90,9118
Polymers89,7372
Non-polymers1,1756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3870 Å2
ΔGint-72 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.036, 89.036, 157.783
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: 44868.320 Da / Num. of mol.: 1 / Mutation: C-terminal fusion to HHHHHH, D236N
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mg/ml protein with 2 mM ATP and 10 mM MgCl2, mixed with 14% PEG8000, 100 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate and 20% glycerol

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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: 3.1→40 Å / Num. obs: 12117 / % possible obs: 100 % / Redundancy: 28.3 % / Biso Wilson estimate: 96.75 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.025 / Rrim(I) all: 0.121 / Χ2: 0.915 / Net I/σ(I): 6.3 / Num. measured all: 343402
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.1-3.2129.411780.850.2740.764100
3.21-3.3429.311620.9350.1680.791000.8980.914
3.34-3.4929.211960.9730.1090.8051000.5820.592
3.49-3.6829.211740.990.0630.8581000.3380.344
3.68-3.912912010.9960.040.9661000.2130.217
3.91-4.2128.911960.9970.0310.9671000.1640.167
4.21-4.6328.612040.9980.0210.9891000.1120.114
4.63-5.328.312190.9990.0170.951000.090.092
5.3-6.6727.812410.9990.0171.0551000.0880.089
6.67-4024.313460.9990.0131.01499.80.0630.065

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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: 3.102→36.065 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.02
RfactorNum. reflection% reflection
Rfree0.2588 1181 9.8 %
Rwork0.2255 --
obs0.2287 12055 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 228.71 Å2 / Biso mean: 90.5944 Å2 / Biso min: 39.33 Å2
Refinement stepCycle: final / Resolution: 3.102→36.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 33 1 2360
Biso mean--90.07 65.36 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012414
X-RAY DIFFRACTIONf_angle_d1.2453273
X-RAY DIFFRACTIONf_chiral_restr0.065359
X-RAY DIFFRACTIONf_plane_restr0.007417
X-RAY DIFFRACTIONf_dihedral_angle_d6.5431431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1024-3.24350.36721460.330813041450100
3.2435-3.41430.33071480.288713411489100
3.4143-3.62810.33561520.253813151467100
3.6281-3.90790.28321470.235513461493100
3.9079-4.30060.2521240.224113621486100
4.3006-4.92160.20921470.188513681515100
4.9216-6.19550.26821680.223413581526100
6.1955-36.06730.22381490.21381480162999

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