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- PDB-9c38: Nir1 NirD domain dimer -

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Basic information

Entry
Database: PDB / ID: 9c38
TitleNir1 NirD domain dimer
ComponentsMembrane-associated phosphatidylinositol transfer protein 3
KeywordsLIPID TRANSPORT / dimerization domain
Function / homology
Function and homology information


Synthesis of PI / phosphatidylinositol transfer activity / glycerophospholipase activity / phosphatidylinositol biosynthetic process / endomembrane system / cell projection / receptor tyrosine kinase binding / cell body / calcium ion binding / lipid binding ...Synthesis of PI / phosphatidylinositol transfer activity / glycerophospholipase activity / phosphatidylinositol biosynthetic process / endomembrane system / cell projection / receptor tyrosine kinase binding / cell body / calcium ion binding / lipid binding / membrane / cytosol / cytoplasm
Similarity search - Function
DDHD domain / DDHD domain / PITM 1-3, LNS2 domain / PITM 1-3, beta-sandwich domain / DDHD domain profile. / DDHD / Phosphatidylinositol transfer protein / LNS2/PITP / LNS2 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Membrane-associated phosphatidylinositol transfer protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRahn, T.A. / Airola, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
CitationJournal: To Be Published
Title: Nir1 NirD domain dimer
Authors: Rahn, T.A. / Lee, W.R. / Li, W.T. / Airola, M.V. / Liou, J.
History
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-associated phosphatidylinositol transfer protein 3


Theoretical massNumber of molelcules
Total (without water)42,2671
Polymers42,2671
Non-polymers00
Water4,828268
1
A: Membrane-associated phosphatidylinositol transfer protein 3

A: Membrane-associated phosphatidylinositol transfer protein 3


Theoretical massNumber of molelcules
Total (without water)84,5342
Polymers84,5342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3650 Å2
ΔGint-30 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.403, 69.403, 150.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-878-

HOH

21A-888-

HOH

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Components

#1: Protein Membrane-associated phosphatidylinositol transfer protein 3 / Phosphatidylinositol transfer protein / membrane-associated 3 / PITPnm 3 / Pyk2 N-terminal domain- ...Phosphatidylinositol transfer protein / membrane-associated 3 / PITPnm 3 / Pyk2 N-terminal domain-interacting receptor 1 / NIR-1


Mass: 42266.859 Da / Num. of mol.: 1 / Mutation: residues 287-342 and 493-531 deleted
Source method: isolated from a genetically manipulated source
Details: truncation of 974 amino acid isoform 1(Uniprot: Q9BZ71-1). This construct has residues 119-286, 343-492, 532-604.
Source: (gene. exp.) Homo sapiens (human) / Gene: PITPNM3, NIR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BZ71
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris, pH 7.5, 8.5% isoproponal, 21% glycerol, 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→29.87 Å / Num. obs: 27623 / % possible obs: 94.95 % / Redundancy: 22.5 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.2789 / Rpim(I) all: 0.06057 / Rrim(I) all: 0.2855 / Net I/σ(I): 6.28
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 23.4 % / Rmerge(I) obs: 2.671 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 2366 / CC1/2: 0.657 / CC star: 0.891 / Rpim(I) all: 0.5606 / Rrim(I) all: 2.73 / % possible all: 87.63

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.87 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 19.681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2034 1370 5.22 %
Rwork0.1717 24889 -
obs0.1734 26259 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.73 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 0 268 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01382501
X-RAY DIFFRACTIONf_angle_d1.0823414
X-RAY DIFFRACTIONf_chiral_restr0.0659390
X-RAY DIFFRACTIONf_plane_restr0.0158436
X-RAY DIFFRACTIONf_dihedral_angle_d5.1323340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.33441150.29232251X-RAY DIFFRACTION87.63
2.02-2.10.3181170.23082292X-RAY DIFFRACTION88.99
2.1-2.20.21391190.20012360X-RAY DIFFRACTION91.81
2.2-2.310.22771210.17542432X-RAY DIFFRACTION93.45
2.31-2.460.19981540.15532417X-RAY DIFFRACTION94.52
2.46-2.650.21240.15072525X-RAY DIFFRACTION96.86
2.65-2.910.18881360.15772559X-RAY DIFFRACTION97.61
2.91-3.330.1881730.15242573X-RAY DIFFRACTION98.99
3.33-4.20.16931500.14042656X-RAY DIFFRACTION99.61
4.2-29.870.19511610.17792824X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 37.2283722294 Å / Origin y: 10.9721772812 Å / Origin z: 70.094406447 Å
111213212223313233
T0.0828730431129 Å2-6.18430746437E-5 Å20.00502528987136 Å2-0.133748468184 Å20.00659403174339 Å2--0.113613577569 Å2
L1.16197047515 °2-0.253314588525 °2-0.343328990428 °2-0.84550028392 °20.0619270800043 °2--1.14642712549 °2
S0.00560986368672 Å °-0.0635049672003 Å °-0.0506680098697 Å °0.00374794464078 Å °-0.0205055384477 Å °-0.0843173817145 Å °0.0907590519029 Å °0.18544416173 Å °0.0101215416569 Å °
Refinement TLS groupSelection details: all

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