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- PDB-3rcp: Crystal structure of the FAPP1 pleckstrin homology domain -

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Basic information

Entry
Database: PDB / ID: 3rcp
TitleCrystal structure of the FAPP1 pleckstrin homology domain
ComponentsPleckstrin homology domain-containing family A member 3
KeywordsMEMBRANE PROTEIN / FAPP1 / PH domain / Lipid-binding / Membrane / seven-stranded-barrel capped by an helix at one edge / phospholipid Binding
Function / homology
Function and homology information


receptor recycling / endosome organization / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / Synthesis of PIPs at the plasma membrane / trans-Golgi network / recycling endosome / early endosome / Golgi membrane / Golgi apparatus ...receptor recycling / endosome organization / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / Synthesis of PIPs at the plasma membrane / trans-Golgi network / recycling endosome / early endosome / Golgi membrane / Golgi apparatus / identical protein binding / cytosol
Similarity search - Function
PH domain containing protein Boi1/Boi2-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Pleckstrin homology domain-containing family A member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRoy, S. / He, J. / Kutateladze, T.G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Basis of Phosphatidylinositol 4-Phosphate and ARF1 GTPase Recognition by the FAPP1 Pleckstrin Homology (PH) Domain.
Authors: He, J. / Scott, J.L. / Heroux, A. / Roy, S. / Lenoir, M. / Overduin, M. / Stahelin, R.V. / Kutateladze, T.G.
History
DepositionMar 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleckstrin homology domain-containing family A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0802
Polymers11,9881
Non-polymers921
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pleckstrin homology domain-containing family A member 3
hetero molecules

A: Pleckstrin homology domain-containing family A member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1604
Polymers23,9762
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3090 Å2
ΔGint-9 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.025, 31.025, 216.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pleckstrin homology domain-containing family A member 3 / PH domain-containing family A member 3 / Phosphatidylinositol-four-phosphate adapter protein 1 / ...PH domain-containing family A member 3 / Phosphatidylinositol-four-phosphate adapter protein 1 / FAPP-1 / Phosphoinositol 4-phosphate adapter protein 1


Mass: 11988.104 Da / Num. of mol.: 1 / Fragment: Residues 1-99, PH domain / Mutation: C94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAPP1, PLEKHA3 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9HB20
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: precipitant solution containing 0.1 M NaAc, pH 4.6, 50mM (NH4)2SO4 and 15% PEG1000., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2010 / Details: mirrors
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30.7118 Å / Num. all: 15767 / Num. obs: 15364 / % possible obs: 96.42 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 35.2 Å2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 6.7 / Num. unique all: 455 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL2Mapmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.826 Å / SU ML: 0.24 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1513 9.85 %Random
Rwork0.2302 ---
all0.265 15767 --
obs0.2328 15364 96.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.281 Å2 / ksol: 0.421 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1745 Å2-0 Å20 Å2
2---4.1745 Å2-0 Å2
3---8.349 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 6 65 877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017829
X-RAY DIFFRACTIONf_angle_d1.5731117
X-RAY DIFFRACTIONf_dihedral_angle_d17.89304
X-RAY DIFFRACTIONf_chiral_restr0.113119
X-RAY DIFFRACTIONf_plane_restr0.01138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.96170.3041350.27261207X-RAY DIFFRACTION92
1.9617-2.03180.26461340.26231188X-RAY DIFFRACTION91
2.0318-2.11310.30731370.24811210X-RAY DIFFRACTION94
2.1131-2.20920.23731370.2311276X-RAY DIFFRACTION95
2.2092-2.32570.28311300.23191239X-RAY DIFFRACTION96
2.3257-2.47130.3361390.24841264X-RAY DIFFRACTION98
2.4713-2.6620.28291300.24611297X-RAY DIFFRACTION98
2.662-2.92970.25451370.2311280X-RAY DIFFRACTION98
2.9297-3.35310.22241460.21471298X-RAY DIFFRACTION99
3.3531-4.22270.21771430.20041290X-RAY DIFFRACTION100
4.2227-29.82990.25151450.23231302X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.1866 Å / Origin y: 11.0703 Å / Origin z: 15.0538 Å
111213212223313233
T0.0989 Å2-0.0008 Å20.0586 Å2-0.1238 Å20.0022 Å2--0.1415 Å2
L0.8327 °2-0.3922 °20.3915 °2-0.2563 °2-0.0948 °2--0.3015 °2
S0.0312 Å °-0.1805 Å °-0.1962 Å °0.0401 Å °0.0787 Å °0.1756 Å °-0.0067 Å °-0.0718 Å °0.3386 Å °
Refinement TLS groupSelection details: chain A

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