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- PDB-5ik8: Laminin A2LG45 I-form, G6/7 bound. -

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Basic information

Entry
Database: PDB / ID: 5ik8
TitleLaminin A2LG45 I-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 / 2 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

Downloads & links

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Assembly

Deposited unit
A: Laminin subunit alpha-2
B: Laminin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,59226
Polyers82,8102
Non-polymers2,78224
Water9,602533
1
A: Laminin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,39511
Polyers41,4051
Non-polymers99010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Laminin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,19815
Polyers41,4051
Non-polymers1,79314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)111.540, 126.290, 144.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI 21 21 21

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Components

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Protein/peptide , 1 types, 2 molecules AB

#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: 41405.023 Da / Num. of mol.: 2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lama2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q60675

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Non-polymers , 8 types, 557 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Formula: Ca / Calcium
#3: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Formula: C6H5O7
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Formula: C2H6O2 / Ethylene glycol
#6: Chemical ChemComp-4MU / 7-hydroxy-4-methyl-2H-chromen-2-one / 4-methylumbelliferone


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


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


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


Mass: 18.015 Da / Num. of mol.: 533 / 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: 3.06 / Density percent sol: 59.83 %
Crystal growTemp: 292 K / Method: vapor diffusion, hanging drop / Details: 100mM Ammonium Citrate diabasic 18% PEG3350

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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: Oct 8, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 55.77 Å / Number obs: 68770 / CC half: 0.999 / Rmerge I obs: 0.088 / NetI over sigmaI: 17.3 / Redundancy: 13.5 % / Percent possible obs: 100
Reflection shellRmerge I obs: 1.64 / Highest resolution: 2 Å / Lowest resolution: 2.07 Å / MeanI over sigI obs: 1.7 / Redundancy: 13.6 % / Percent possible all: 99.9

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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: 0.27 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 22.11
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2095 / R factor R work: 0.177 / R factor obs: 0.1786 / Highest resolution: 2 Å / Lowest resolution: 55.77 Å / Number reflection R free: 3436 / Number reflection obs: 68768 / Percent reflection R free: 5 / Percent reflection obs: 99.99
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 55.77 Å
Number of atoms included #LASTProtein: 5755 / Nucleic acid: 0 / Ligand: 175 / Solvent: 533 / Total: 6463
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096073
X-RAY DIFFRACTIONf_angle_d0.6648203
X-RAY DIFFRACTIONf_dihedral_angle_d11.9123586
X-RAY DIFFRACTIONf_chiral_restr0.069933
X-RAY DIFFRACTIONf_plane_restr0.0031068
Refine LS shell

Refine ID: X-RAY DIFFRACTION / Percent reflection obs: 1

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R work
2.00000.36820.28482.02741432585
2.02740.30080.27812.05641482569
2.05640.32240.26172.08711462573
2.08710.27930.24972.11971272599
2.11970.25620.22982.15441412563
2.15440.27680.22362.19161332622
2.19160.26150.21772.23141392561
2.23140.24930.20892.27431342612
2.27430.23580.20602.32081362591
2.32080.28970.20962.37121242586
2.37120.24680.20622.42641172612
2.42640.25260.19802.48711362602
2.48710.24300.19002.55431242609
2.55430.25440.19282.62951222641
2.62950.23440.19652.71441312606
2.71440.23290.19642.81141442571
2.81140.24680.19692.92391402622
2.92390.25150.19213.05701322614
3.05700.26590.18893.21811252631
3.21810.20040.17583.41971352625
3.41970.16120.15803.68371502633
3.68370.17330.14474.05431562607
4.05430.15720.12534.64081482652
4.64080.18010.14165.84591542674
5.84590.20620.194355.79171512772
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
12.8617-0.77840.02591.39660.75860.9368-0.1463-0.23160.29320.1089-0.02950.3194-0.0119-0.19420.19070.40830.03140.07810.36440.02120.4995-30.549024.453045.2682
22.14670.6100-0.21211.5710-0.07852.29110.03390.17320.1737-0.00220.05440.0043-0.1700-0.1168-0.08550.36540.06110.02450.27870.03880.3480-3.661113.596824.4349
35.7194-0.99320.90542.93970.23742.6032-0.6380-0.49910.82130.21400.0512-0.6968-0.32350.13070.33510.6201-0.0559-0.19160.43620.02160.7123-29.276876.311417.2087
43.4466-0.55651.10072.5209-0.42342.7027-0.1272-0.51960.22330.07850.13310.3556-0.5896-0.98150.14810.47950.2172-0.08190.7507-0.15770.4043-58.544473.53788.7945
53.13860.43260.85482.33830.15252.8841-0.1870-0.09160.1565-0.03770.02900.2463-0.3155-0.75860.15590.40770.1275-0.05900.6556-0.08560.3646-59.330368.47562.0967
62.8395-0.89021.11280.4638-0.58972.0335-0.1844-0.06290.21060.1265-0.06150.0592-0.5708-0.71960.23260.52430.1266-0.06570.5716-0.12090.3514-42.264670.136718.1615
72.4575-1.04870.07552.63990.34932.0048-0.00770.0225-0.25170.2408-0.10170.04180.1550-0.08050.08430.3575-0.0404-0.03220.3128-0.02450.3246-23.484850.902023.2802
82.8006-1.04730.58203.08020.14172.35200.09880.2469-0.1234-0.1580-0.23420.3538-0.0332-0.41780.17980.3663-0.0180-0.03130.4439-0.04750.3374-34.870358.395518.4980
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2738 through 2944 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2945 through 3118 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2741 through 2760 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2761 through 2790 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2791 through 2917 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2918 through 2947 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2948 through 3075 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3076 through 3118 )

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