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

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Basic information

Entry
Database: PDB / ID: 6cmw
TitleCrystal structure of zebrafish Phosphatidylinositol-4-phosphate 5- kinase alpha isoform with bound ATP/Ca2+
ComponentsPhosphatidylinositol-4-phosphate 5-kinase, type I, alpha
KeywordsTRANSFERASE / ATP / PIP5ka
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
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: 3.15 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 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
SupersessionMar 21, 2018ID: 5C3V
Revision 1.1Mar 21, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_database_PDB_obs_spr / Item: _audit_author.identifier_ORCID
Revision 1.2Apr 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 1.3Oct 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

Downloads & links

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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)45,4574
Polymers44,8691
Non-polymers5873
Water00
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)90,9138
Polymers89,7392
Non-polymers1,1756
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4160 Å2
ΔGint-75 kcal/mol
Surface area27910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.590, 88.590, 157.484
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: 44869.309 Da / Num. of mol.: 1 / Mutation: C-terminal fusion to HHHHHH
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

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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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 277 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: 1.078 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 3.15→40 Å / Num. obs: 11470 / % possible obs: 100 % / Redundancy: 28.2 % / Biso Wilson estimate: 91.03 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.02 / Rrim(I) all: 0.105 / Χ2: 0.963 / Net I/σ(I): 8.2 / Num. measured all: 323007
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.26290.89310980.9440.1680.9090.818100
3.26-3.3928.90.57411130.9780.1080.5850.854100
3.39-3.5528.90.39611350.990.0750.4030.945100
3.55-3.7328.80.24711080.9950.0470.2521.08100
3.73-3.9728.80.16911270.9970.0320.1720.942100
3.97-4.2728.80.12411340.9980.0240.1270.915100
4.27-4.728.40.10111430.9980.0190.1021.00899.9
4.7-5.3828.20.07811570.9990.0150.0791.048100
5.38-6.7827.60.07111760.9990.0140.0731.049100
6.78-4024.70.046127910.0090.0470.96899.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZ7

4tz7


Resolution: 3.15→35.978 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.04
RfactorNum. reflection% reflection
Rfree0.2602 1152 10.09 %
Rwork0.208 --
obs0.2133 11412 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.18 Å2 / Biso mean: 81.17 Å2 / Biso min: 35.44 Å2
Refinement stepCycle: final / Resolution: 3.15→35.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 33 0 2394
Biso mean--67.81 --
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012452
X-RAY DIFFRACTIONf_angle_d1.3693329
X-RAY DIFFRACTIONf_chiral_restr0.053364
X-RAY DIFFRACTIONf_plane_restr0.006427
X-RAY DIFFRACTIONf_dihedral_angle_d16.613875
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1483-3.29150.35651250.305612661391
3.2915-3.46490.31941630.271112161379
3.4649-3.68180.34131400.232512631403
3.6818-3.96580.28361220.233812751397
3.9658-4.36430.26021650.194612441409
4.3643-4.99430.20321580.169912691427
4.9943-6.28690.28291330.204813331466
6.2869-35.98040.22931460.193513941540

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