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- PDB-5y30: Crystal structure of LGI1 LRR domain -

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Basic information

Entry
Database: PDB / ID: 5y30
TitleCrystal structure of LGI1 LRR domain
ComponentsLeucine-rich glioma-inactivated protein 1
KeywordsCELL ADHESION / epilepsy / synapse / ADAM / EPTP / WD40
Function / homology
Function and homology information


LGI-ADAM interactions / axon initial segment / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / myelination / axon guidance / neuron projection development / nervous system development / positive regulation of cell growth ...LGI-ADAM interactions / axon initial segment / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / myelination / axon guidance / neuron projection development / nervous system development / positive regulation of cell growth / signaling receptor binding / glutamatergic synapse / dendrite / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Leucine-rich glioma-inactivated , EPTP repeat / EAR / EPTP domain / EAR repeat profile. / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich glioma-inactivated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsYamagata, A. / Fukai, S.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22.
Authors: Yamagata, A. / Miyazaki, Y. / Yokoi, N. / Shigematsu, H. / Sato, Y. / Goto-Ito, S. / Maeda, A. / Goto, T. / Sanbo, M. / Hirabayashi, M. / Shirouzu, M. / Fukata, Y. / Fukata, M. / Fukai, S.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Leucine-rich glioma-inactivated protein 1


Theoretical massNumber of molelcules
Total (without water)23,8081
Polymers23,8081
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9430 Å2
Unit cell
Length a, b, c (Å)65.252, 65.252, 109.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Leucine-rich glioma-inactivated protein 1 / Epitempin-1


Mass: 23808.107 Da / Num. of mol.: 1 / Fragment: LGI1 LRR domain (UNP RESIDUES 37-223)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGI1, EPT, UNQ775/PRO1569 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: O95970
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 4000, 0.2 M ammonium acetate, 0.1 M tri-sodium citrate (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 25330 / % possible obs: 99.9 % / Redundancy: 15.1 % / Rsym value: 0.055 / Net I/σ(I): 47.2
Reflection shellResolution: 1.78→1.81 Å / Mean I/σ(I) obs: 2.2 / CC1/2: 0.558 / Rsym value: 0.45 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WFH

2wfh


Resolution: 1.781→39.366 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 20.38
RfactorNum. reflection% reflection
Rfree0.1911 1234 4.88 %
Rwork0.1655 --
obs0.1667 25295 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.781→39.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 100 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081501
X-RAY DIFFRACTIONf_angle_d1.1032041
X-RAY DIFFRACTIONf_dihedral_angle_d12.135558
X-RAY DIFFRACTIONf_chiral_restr0.044238
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.781-1.85230.30511300.28092683X-RAY DIFFRACTION100
1.8523-1.93660.24261290.23412654X-RAY DIFFRACTION100
1.9366-2.03870.24991290.19722679X-RAY DIFFRACTION100
2.0387-2.16640.19481330.17352669X-RAY DIFFRACTION100
2.1664-2.33370.20511560.16662654X-RAY DIFFRACTION100
2.3337-2.56850.21121470.16452647X-RAY DIFFRACTION100
2.5685-2.94010.21771330.17782680X-RAY DIFFRACTION100
2.9401-3.70370.18291400.16452682X-RAY DIFFRACTION100
3.7037-39.37570.15821370.14142713X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.5236 Å / Origin y: 21.0476 Å / Origin z: -0.7258 Å
111213212223313233
T0.2217 Å20.0105 Å20.0178 Å2-0.1925 Å20.0267 Å2--0.1616 Å2
L3.4996 °2-1.0605 °2-0.1852 °2-3.8773 °20.3285 °2--3.7867 °2
S0.0117 Å °0.1104 Å °0.265 Å °-0.0934 Å °0.0286 Å °-0.1261 Å °-0.3393 Å °-0.0847 Å °-0.0049 Å °
Refinement TLS groupSelection details: all

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