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- PDB-6f2o: Crystal structure of mouse SALM5 adhesion protein extracellular L... -

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Basic information

Entry
Database: PDB / ID: 6f2o
TitleCrystal structure of mouse SALM5 adhesion protein extracellular LRR-Ig domain fragment
ComponentsLeucine-rich repeat and fibronectin type-III domain-containing protein 5
KeywordsCELL ADHESION / Synapse / leucine rich repeat
Function / homology
Function and homology information


negative regulation of macrophage activation / synaptic membrane adhesion / regulation of presynapse assembly / GABA-ergic synapse / postsynaptic density membrane / negative regulation of inflammatory response / glutamatergic synapse / cell surface
Similarity search - Function
Leucine-rich repeat and fibronectin type-III domain-containing protein 5 / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 ...Leucine-rich repeat and fibronectin type-III domain-containing protein 5 / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine-rich repeat profile. / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Leucine-rich repeat domain superfamily / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Leucine-rich repeat and fibronectin type-III domain-containing protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKarki, S. / Paudel, P. / Sele, C. / Kajander, T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Protein Eng. Des. Sel. / Year: 2018
Title: The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition.
Authors: Karki, S. / Paudel, P. / Sele, C. / Shkumatov, A.V. / Kajander, T.
History
DepositionNov 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich repeat and fibronectin type-III domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)43,5191
Polymers43,5191
Non-polymers00
Water00
1
A: Leucine-rich repeat and fibronectin type-III domain-containing protein 5

A: Leucine-rich repeat and fibronectin type-III domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)87,0382
Polymers87,0382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation42_554-x+3/4,z+1/4,y-1/41
Unit cell
Length a, b, c (Å)254.015, 254.015, 254.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein Leucine-rich repeat and fibronectin type-III domain-containing protein 5


Mass: 43519.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrfn5, Kiaa4208, Salm5 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8BXA0

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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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14488 / % possible obs: 98.8 % / Redundancy: 11.03 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 10.59
Reflection shellResolution: 3→3.18 Å / Redundancy: 11.47 % / Rmerge(I) obs: 2.226 / Mean I/σ(I) obs: 1.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.94 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.552 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.568 / SU Rfree Blow DPI: 0.348 / SU Rfree Cruickshank DPI: 0.349
RfactorNum. reflection% reflectionSelection details
Rfree0.282 721 4.99 %RANDOM
Rwork0.252 ---
obs0.253 14438 99.1 %-
Displacement parametersBiso mean: 142.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 3→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 0 0 2457
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112509HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.363435HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d816SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes366HARMONIC5
X-RAY DIFFRACTIONt_it2509HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion22.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion362SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2653SEMIHARMONIC4
LS refinement shellResolution: 3→3.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.345 146 4.99 %
Rwork0.325 2780 -
all0.326 2926 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 105.857 Å / Origin y: 134.077 Å / Origin z: 52.1637 Å
111213212223313233
T-0.1684 Å2-0.304 Å2-0.0017 Å2-0.0406 Å20.192 Å2---0.1988 Å2
L1.8781 °2-1.4729 °20.9721 °2-5.8501 °2-1.6978 °2--1.429 °2
S-0.5783 Å °0.4151 Å °0.4995 Å °0.1338 Å °0.2342 Å °-0.4489 Å °-0.3566 Å °0.3824 Å °0.3441 Å °
Refinement TLS groupSelection details: { A|* }

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