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- PDB-2wwe: Crystal structure of the phox homology domain of human phosphoino... -

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Basic information

Entry
Database: PDB / ID: 2wwe
TitleCrystal structure of the phox homology domain of human phosphoinositide-3-kinase-C2-gamma
ComponentsPHOSPHOINOSITIDE-3-KINASE, CLASS 2, GAMMA POLYPEPTIDE
KeywordsTRANSFERASE / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / KINASE / PIK3C2G / MEMBRANE / PX-DOMAIN / ATP-BINDING / POLYMORPHISM / CLASS 2 PI3K
Function / homology
Function and homology information


: / : / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4-phosphate 3-kinase / phosphatidylinositol kinase activity / phosphatidylinositol biosynthetic process / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity ...: / : / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4-phosphate 3-kinase / phosphatidylinositol kinase activity / phosphatidylinositol biosynthetic process / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol binding / chemotaxis / cell migration / viral RNA genome replication / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PI3K-C2-gamma, catalytic domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain ...PI3K-C2-gamma, catalytic domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit gamma / Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsRoos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Kraulis, P. / Markova, N. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the Phox Homology Domain of Human Phosphoinositide-3-Kinase-C2-Gamma
Authors: Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Kraulis, P. / Markova, N. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
History
DepositionOct 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Derived calculations / Refinement description / Version format compliance
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOINOSITIDE-3-KINASE, CLASS 2, GAMMA POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)14,9781
Polymers14,9781
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.420, 53.420, 75.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PHOSPHOINOSITIDE-3-KINASE, CLASS 2, GAMMA POLYPEPTIDE


Mass: 14977.646 Da / Num. of mol.: 1 / Fragment: PHOX HOMOLOGY DOMAIN, RESIDUES 1203-1306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE / References: UniProt: A1L3U0, UniProt: O75747*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1M TRI-SODIUM CITRATE DIHYDRATE PH 5.5, 20% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9789
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.25→29.16 Å / Num. obs: 34900 / % possible obs: 99.9 % / Observed criterion σ(I): 4.5 / Redundancy: 8.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2AR5, 2IWL,1O7K, 2V6V

2ar5

2iwl

1o7k

2v6v


Resolution: 1.25→26.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.556 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18398 1772 5.1 %RANDOM
Rwork0.16502 ---
obs0.16596 33091 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 0 175 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211002
X-RAY DIFFRACTIONr_bond_other_d0.0010.02673
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9141367
X-RAY DIFFRACTIONr_angle_other_deg1.63131645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1485126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.92624.28656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45515174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.613155
X-RAY DIFFRACTIONr_chiral_restr0.0840.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
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_it0.8311.5586
X-RAY DIFFRACTIONr_mcbond_other0.2051.5229
X-RAY DIFFRACTIONr_mcangle_it1.5262958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1653416
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5144.5401
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 131 -
Rwork0.255 2385 -
obs--98.78 %

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