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- PDB-1t27: THE STRUCTURE OF PITP COMPLEXED TO PHOSPHATIDYLCHOLINE -

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Basic information

Entry
Database: PDB / ID: 1t27
TitleTHE STRUCTURE OF PITP COMPLEXED TO PHOSPHATIDYLCHOLINE
ComponentsPhosphatidylinositol transfer protein alpha isoform
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


stearic acid binding / phosphatidylcholine transporter activity / phosphatidylinositol transfer activity / fatty-acyl-CoA binding / phosphatidylcholine binding / phospholipid transport / phosphatidylinositol binding / axonogenesis / phospholipid binding / cytoplasm
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
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Phosphatidylinositol transfer protein alpha isoform
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsYoder, M.D. / Thomas, L.M. / Tremblay, J.M. / Oliver, R.L. / Yarbrough, L.R. / Helmkamp Jr., G.M.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: STRUCTURE OF A MULTIFUNCTIONAL PROTEIN. MAMMALIAN PHOSPHATIDYLINOSITOL TRANSFER PROTEIN COMPLEXED WITH PHOSPHATIDYLCHOLINE
Authors: Yoder, M.D. / Thomas, L.M. / Tremblay, J.M. / Oliver, R.L. / Yarbrough, L.R. / Helmkamp Jr., G.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: X-RAY ANALYSIS OF CRYSTALS OF RAT PHOSPHATIDYLINOSITOL-TRANSFER PROTEIN WITH BOUND PHOSPHATIDYLCHOLINE
Authors: Oliver, R.L. / Tremblay, J.M. / Helmkamp Jr., G.M. / Yarbrough, L.R. / Breakfield, N.W. / Yoder, M.D.
History
DepositionApr 20, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMay 11, 2004ID: 1FVZ
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol transfer protein alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7432
Polymers31,9551
Non-polymers7871
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.914, 73.773, 48.185
Angle α, β, γ (deg.)90.00, 114.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphatidylinositol transfer protein alpha isoform / PtdIns transfer protein alpha / PtdInsTP / PI-TP-alpha


Mass: 31955.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PITPN, PITPNA / Organ: brain / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P16446
#2: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, sodium acetate, Tris-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9791, 0.9794, 0.9500
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Nov 18, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.951
ReflectionResolution: 2.2→50 Å / Num. all: 38629 / Num. obs: 38629 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.2
Reflection shellResolution: 2.2→50 Å / Rmerge(I) obs: 0.081 / % possible all: 67.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.94 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1407892.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 629 5.2 %RANDOM
Rwork0.205 ---
all0.205 13081 --
obs0.205 12145 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3224 Å2 / ksol: 0.338776 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20.99 Å2
2---2.08 Å20 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 54 144 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 67 4.6 %
Rwork0.202 1396 -
obs--62.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PCO.PARPCO.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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