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- PDB-5ik5: Laminin A2LG45 C-form, G6/7 bound. -

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Basic information

Entry
Database: PDB / ID: 5ik5
TitleLaminin A2LG45 C-form, G6/7 bound.
ComponentsLaminin subunit alpha-2
KeywordsSTRUCTURAL PROTEIN / Extracellular Matrix / Ligand binding / LG domain / structural protein
Function / homologyGrowth factor receptor cysteine-rich domain superfamily / Laminin N-terminal (Domain VI) / Laminin alpha, domain I / Laminin domain II / Concanavalin A-like lectin/glucanase domain superfamily / Laminin, N-terminal domain superfamily / Laminin B (Domain IV) / Laminin EGF domain / Laminin G domain / Laminin G domain ...Growth factor receptor cysteine-rich domain superfamily / Laminin N-terminal (Domain VI) / Laminin alpha, domain I / Laminin domain II / Concanavalin A-like lectin/glucanase domain superfamily / Laminin, N-terminal domain superfamily / Laminin B (Domain IV) / Laminin EGF domain / Laminin G domain / Laminin G domain / Laminin N-terminal domain profile. / Laminin Domain I / Laminin Domain II / EGF-like domain signature 1. / EGF-like domain signature 2. / Laminin-type EGF-like (LE) domain signature. / Laminin G domain profile. / Laminin-type EGF-like (LE) domain profile. / Laminin, N-terminal / Laminin EGF domain / Laminin G domain / EGF-like domain / MET activates PTK2 signaling / Laminin interactions / Laminin IV type A domain profile. / Laminin IV / positive regulation of synaptic transmission, cholinergic / Schwann cell differentiation / regulation of embryonic development / extracellular matrix structural constituent / regulation of cell adhesion / synaptic cleft / basement membrane / regulation of cell migration / sarcolemma / neuromuscular junction / axon guidance / collagen-containing extracellular matrix / dendritic spine / cell adhesion / signaling receptor binding / extracellular space / extracellular region / Laminin subunit alpha-2
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.39 Å resolution
AuthorsBriggs, D.C. / Hohenester, E. / Campbell, K.P.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural basis of laminin binding to the LARGE glycans on dystroglycan.
Authors: Briggs, D.C. / Yoshida-Moriguchi, T. / Zheng, T. / Venzke, D. / Anderson, M.E. / Strazzulli, A. / Moracci, M. / Yu, L. / Hohenester, E. / Campbell, K.P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 3, 2016 / Release: Aug 10, 2016
RevisionDateData content typeGroupProviderType
1.0Aug 10, 2016Structure modelrepositoryInitial release
1.1Aug 24, 2016Structure modelDatabase references
1.2Sep 28, 2016Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laminin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,97018
Polyers42,6281
Non-polymers2,34117
Water8,287460
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)70.390, 110.740, 123.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Laminin subunit alpha-2 / / Laminin M chain / Laminin-12 subunit alpha / Laminin-2 subunit alpha / Laminin-4 subunit alpha / Merosin heavy chain


Mass: 42628.438 Da / Num. of mol.: 1 / Fragment: UNP residues 2730-3118 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lama2 / Plasmid name: pCEP-Pu / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q60675

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Non-polymers , 9 types, 477 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#3: Chemical ChemComp-A2G / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
#4: Chemical ChemComp-GAL / BETA-D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6 / Galactose
#5: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Formula: C3H8O3 / Glycerol
#7: Chemical ChemComp-4MU / 7-hydroxy-4-methyl-2H-chromen-2-one / 4-methylumbelliferone


Mass: 176.169 Da / Num. of mol.: 1 / Formula: C10H8O3 / Hymecromone
#8: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#9: Chemical ChemComp-XYS / XYLOPYRANOSE


Mass: 150.130 Da / Num. of mol.: 2 / Formula: C5H10O5
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Formula: H2O / Water

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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 / Density percent sol: 56.57 %
Crystal growTemp: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES/MOPS 120mM Glucuronic Acid 30% PEG8k/Glycerol mix

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: DIAMOND BEAMLINE I02 / Synchrotron site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Collection date: May 14, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 18.04 Å2 / D resolution high: 1.39 Å / D resolution low: 61.95 Å / Number obs: 81183 / CC half: 0.999 / Rmerge I obs: 0.035 / NetI over sigmaI: 17.3 / Redundancy: 3.9 % / Percent possible obs: 83.7
Reflection shellRmerge I obs: 0.422 / Highest resolution: 1.39 Å / Lowest resolution: 1.44 Å / MeanI over sigI obs: 1.3 / Redundancy: 1.6 % / Percent possible all: 35.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYK
Overall SU ML: 0.13 / R Free selection details: Random Selection / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 22.15 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.1768 / R factor R work: 0.1489 / R factor obs: 0.1504 / Highest resolution: 1.39 Å / Lowest resolution: 61.95 Å / Number reflection R free: 4052 / Number reflection obs: 81182 / Percent reflection R free: 4.99 / Percent reflection obs: 83.5
Refine hist #LASTHighest resolution: 1.39 Å / Lowest resolution: 61.95 Å
Number of atoms included #LASTProtein: 2888 / Nucleic acid: 0 / Ligand: 146 / Solvent: 460 / Total: 3494
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123182
X-RAY DIFFRACTIONf_angle_d0.8954310
X-RAY DIFFRACTIONf_dihedral_angle_d15.2241204
X-RAY DIFFRACTIONf_chiral_restr0.079503
X-RAY DIFFRACTIONf_plane_restr0.005543
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.39000.30500.26331.40645099532.00
1.40640.28250.25491.423551122138.00
1.42350.29360.23271.441570132542.00
1.44150.30730.22571.460563154848.00
1.46050.27110.20961.480578165952.00
1.48050.26480.19931.5017103181758.00
1.50170.24580.19321.5241101196062.00
1.52410.22410.18841.5479120211268.00
1.54790.22960.16981.5733129232674.00
1.57330.22260.15891.6004127251978.00
1.60040.24780.16011.6295135268486.00
1.62950.19820.15581.6609141288291.00
1.66090.19270.15721.6948144305596.00
1.69480.19940.15161.73161713155100.00
1.73160.20920.15001.77191943135100.00
1.77190.19170.14831.81621323211100.00
1.81620.18430.14281.86531633167100.00
1.86530.20210.14181.92021553165100.00
1.92020.16060.13831.9822185315099.00
1.98220.13930.13522.05311623177100.00
2.05310.18410.13622.13531503188100.00
2.13530.15910.13482.23241773163100.00
2.23240.16260.14572.35011603205100.00
2.35010.17040.14462.4974156317699.00
2.49740.18770.15572.69021483221100.00
2.69020.18910.14922.96091783211100.00
2.96090.18820.14623.3894193316699.00
3.38940.15200.13334.2701198322399.00
4.27010.16190.160362.0116218331499.00

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