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- PDB-4cbp: Crystal structure of neural ectodermal development factor IMP-L2. -

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Basic information

Entry
Database: PDB / ID: 4cbp
TitleCrystal structure of neural ectodermal development factor IMP-L2.
ComponentsNEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2
KeywordsCELL ADHESION / IMAGINAL MORPHOGENESIS PROTEIN-LATE 2 / INSULIN BINDING / IMMUNOGLOBULIN DOMAIN / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


positive regulation of entry into reproductive diapause / dendrite self-avoidance / cell-cell adhesion mediator activity / insulin binding / response to starvation / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of lipid storage / positive regulation of insulin receptor signaling pathway / negative regulation of insulin receptor signaling pathway / determination of adult lifespan ...positive regulation of entry into reproductive diapause / dendrite self-avoidance / cell-cell adhesion mediator activity / insulin binding / response to starvation / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of lipid storage / positive regulation of insulin receptor signaling pathway / negative regulation of insulin receptor signaling pathway / determination of adult lifespan / axon guidance / axon / extracellular space / plasma membrane
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural/ectodermal development factor IMP-L2
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKulahin, N. / Kristensen, O. / Brzozowski, M. / Schluckebier, G. / Meyts, P.D.
CitationJournal: To be Published
Title: Structural Analysis of Imp-L2 Function
Authors: Kulahin, N. / Watson, C.J. / Turkenburg, J.P. / Kristensen, O. / Norrman, M. / Sajid, W. / Schluckebier, G. / Meyts, P.D. / Brzozowski, M.
History
DepositionOct 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.2May 29, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2
B: NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8354
Polymers60,6512
Non-polymers1842
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-5.4 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.856, 99.732, 56.280
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9872, -0.157, 0.0295), (-0.1518, 0.9794, 0.1329), (-0.0497, 0.1267, -0.9907)7.294, -10.722, 118.3484

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Components

#1: Protein NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2 / NEURAL ECTODERMAL DEVELOPMENT FACTOR IMP-L2


Mass: 30325.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q09024
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: HANGING-DROP EXPERIMENTS BY MIXING 1 UL PROTEIN (5.5. MG/ML IN 10 MM HEPES PH 7.4, 20 MM NACL) AND 1 UL RESERVOIR SOLUTION (17% PEG-6000, 0.1 M TRIS HYDROCHLORIDE, PH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.59→56.25 Å / Num. obs: 70546 / % possible obs: 95.7 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.4
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 71.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
MOSFLMdata reduction
xia2data scaling
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→29.542 Å / SU ML: 0.16 / σ(F): 1.91 / Phase error: 18.62 / Stereochemistry target values: ML / Details: REFINED AGAINST ANOMALOUS DATA
RfactorNum. reflection% reflection
Rfree0.1883 3844 2.8 %
Rwork0.1562 --
obs0.1571 69600 94.74 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→29.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 12 457 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063495
X-RAY DIFFRACTIONf_angle_d1.0864762
X-RAY DIFFRACTIONf_dihedral_angle_d11.7821321
X-RAY DIFFRACTIONf_chiral_restr0.04535
X-RAY DIFFRACTIONf_plane_restr0.004621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62910.2821330.23694669X-RAY DIFFRACTION65
1.6291-1.66040.26381700.21995512X-RAY DIFFRACTION74
1.6604-1.69430.2451730.20645908X-RAY DIFFRACTION82
1.6943-1.73120.2182000.18556518X-RAY DIFFRACTION89
1.7312-1.77140.23151980.16836992X-RAY DIFFRACTION95
1.7714-1.81570.20192080.16217303X-RAY DIFFRACTION100
1.8157-1.86480.16782250.15077219X-RAY DIFFRACTION100
1.8648-1.91970.19242130.14027327X-RAY DIFFRACTION100
1.9197-1.98160.1652100.1337258X-RAY DIFFRACTION100
1.9816-2.05240.17762100.13157291X-RAY DIFFRACTION100
2.0524-2.13460.182100.13437284X-RAY DIFFRACTION100
2.1346-2.23170.15622000.13237351X-RAY DIFFRACTION100
2.2317-2.34930.19262070.1397335X-RAY DIFFRACTION100
2.3493-2.49640.1672200.15437290X-RAY DIFFRACTION100
2.4964-2.68910.22382110.15977316X-RAY DIFFRACTION100
2.6891-2.95950.20542160.16317320X-RAY DIFFRACTION100
2.9595-3.38720.18342040.15737286X-RAY DIFFRACTION100
3.3872-4.26540.16632160.15537304X-RAY DIFFRACTION100
4.2654-29.54740.19532200.16847113X-RAY DIFFRACTION97

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