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- PDB-8hpx: Structure of mouse LGI1 LRR domain in space group P65 -

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Basic information

Entry
Database: PDB / ID: 8hpx
TitleStructure of mouse LGI1 LRR domain in space group P65
ComponentsLeucine-rich glioma-inactivated protein 1
KeywordsSIGNALING PROTEIN / Synaptic modulator / LRR domain
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 / axon guidance / positive regulation of cell growth / signaling receptor binding / glutamatergic synapse / dendrite ...LGI-ADAM interactions / axon initial segment / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / axon guidance / positive regulation of cell growth / signaling receptor binding / glutamatergic synapse / dendrite / Golgi apparatus / endoplasmic reticulum / extracellular space / 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 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.68 Å
AuthorsLiu, H. / Xu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31270767 China
CitationJournal: To Be Published
Title: Structure of mouse LGI1 LRR domain in space group P65
Authors: Liu, H. / Xu, F.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich glioma-inactivated protein 1
B: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2994
Polymers45,8562
Non-polymers4422
Water00
1
A: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers22,9281
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine-rich glioma-inactivated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers22,9281
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.952, 90.952, 191.228
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 22928.094 Da / Num. of mol.: 2 / Fragment: LRR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgi1 / Production host: Homo sapiens (human) / References: UniProt: Q9JIA1
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: 4.98 Å3/Da / Density % sol: 75.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.6M sodium citrate, 0.1M sodium cacodylate pH=6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.68→50 Å / Num. obs: 9697 / % possible obs: 98.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.059 / Rsym value: 0.037 / Net I/σ(I): 39.866
Reflection shellResolution: 3.68→3.82 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2.415 / Num. unique obs: 445 / Rsym value: 0.737 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K3S

6k3s
PDB Unreleased entry


Resolution: 3.68→45.48 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.83
RfactorNum. reflection% reflection
Rfree0.251 461 4.77 %
Rwork0.22 --
obs0.222 9663 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.68→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 28 0 2882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032958
X-RAY DIFFRACTIONf_angle_d0.8474022
X-RAY DIFFRACTIONf_dihedral_angle_d12.9931112
X-RAY DIFFRACTIONf_chiral_restr0.057462
X-RAY DIFFRACTIONf_plane_restr0.004516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.68-4.20740.2761620.26733072X-RAY DIFFRACTION100
4.2074-5.29960.2981620.26743093X-RAY DIFFRACTION100
5.2996-45.47950.23061370.19453037X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -25.1236 Å / Origin y: -22.1997 Å / Origin z: -1.6174 Å
111213212223313233
T1.2246 Å20.093 Å2-0.0375 Å2-1.1183 Å2-0.1705 Å2--1.0815 Å2
L3.7731 °2-1.9078 °20.4913 °2-4.4028 °21.022 °2--3.6829 °2
S-0.4371 Å °0.3018 Å °-0.1345 Å °0.3556 Å °0.3619 Å °-0.1369 Å °-0.1951 Å °-0.2866 Å °0.0691 Å °
Refinement TLS groupSelection details: ALL

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