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- PDB-1kcm: Crystal Structure of Mouse PITP Alpha Void of Bound Phospholipid ... -

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Basic information

Entry
Database: PDB / ID: 1kcm
TitleCrystal Structure of Mouse PITP Alpha Void of Bound Phospholipid at 2.0 Angstroms Resolution
ComponentsPhosphatidylinositol Transfer Protein alpha
KeywordsLIPID BINDING PROTEIN / PITP / phospholipid binding protein / phospholipid transport
Function / homology
Function and homology information


phosphatidylcholine transfer activity / phosphatidylinositol transfer activity / phosphatidylcholine binding / phosphatidylinositol binding / axonogenesis / phospholipid binding / myelin sheath / lipid binding / nucleus / membrane ...phosphatidylcholine transfer activity / phosphatidylinositol transfer activity / phosphatidylcholine binding / phosphatidylinositol binding / axonogenesis / phospholipid binding / myelin sheath / lipid binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / Phosphatidylinositol transfer protein / Phosphatidylinositol transfer protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol transfer protein alpha isoform
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchouten, A. / Agianian, B. / Westerman, J. / Kroon, J. / Wirtz, K.W.A. / Gros, P.
CitationJournal: EMBO J. / Year: 2002
Title: Structure of apo-phosphatidylinositol transfer protein alpha provides insight into membrane association.
Authors: Schouten, A. / Agianian, B. / Westerman, J. / Kroon, J. / Wirtz, K.W. / Gros, P.
History
DepositionNov 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 Transfer Protein alpha


Theoretical massNumber of molelcules
Total (without water)31,8101
Polymers31,8101
Non-polymers00
Water3,891216
1
A: Phosphatidylinositol Transfer Protein alpha

A: Phosphatidylinositol Transfer Protein alpha


Theoretical massNumber of molelcules
Total (without water)63,6202
Polymers63,6202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area27970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.464, 50.464, 216.105
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a homodimer generated from the monomer in the asymmetric unit by the operation: y, x, -z

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Components

#1: Protein Phosphatidylinositol Transfer Protein alpha / PITP alpha


Mass: 31810.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Plasmid details: PET3D CONTAINED PITP cDNA from Swiss mouse 3T3 fibroblast cells
Plasmid: pET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53810
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% PEG 6000, 0.2M calcium acetate, 100MM cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
210 mMTris-HCl1droppH7.2
310 mMbeta-mercaptoethanol1drop
411 %(w/v)PEG60001reservoir
5200 mMcalcium acetate1reservoir
6100 mMcacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9322 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 9, 1999 / Details: Toroidal mirror
RadiationMonochromator: LN2 cooled Si(311) or Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. all: 22808 / Num. obs: 22060 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 25.7
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 7.3 / Num. unique all: 2209 / Rsym value: 0.171 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 4.33 % / Num. measured all: 231585 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 91.1 % / Redundancy: 2.7 % / Num. unique obs: 2012 / Rmerge(I) obs: 0.171

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVZ

1fvz
PDB Unreleased entry


Resolution: 2→30 Å / SU B: 4.23065 / SU ML: 0.12169 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.20144 / ESU R Free: 0.18838
Stereochemistry target values: Engh & Huber, mon_lib (CCP4: Library)
Details: Used maximum likelihood refinement, and TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 1114 5.1 %RANDOM
Rwork0.2159 ---
all0.2188 20780 --
obs0.2188 20780 96.9 %-
Displacement parametersBiso mean: 24.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.43 Å20 Å2
2--0.85 Å20 Å2
3----1.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1884 Å0.2014 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 0 216 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.021
X-RAY DIFFRACTIONp_mcbond_it0.4351.5
X-RAY DIFFRACTIONp_mcangle_it0.8222
X-RAY DIFFRACTIONp_scbond_it1.1513
X-RAY DIFFRACTIONp_scangle_it1.9124.5
X-RAY DIFFRACTIONp_angle_d1.419
X-RAY DIFFRACTIONp_chiral_restr0.1030.2
X-RAY DIFFRACTIONp_plane_restr0.0050.02
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor all: 0.2188 / Rfactor obs: 0.216 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 1.42

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