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- PDB-1qu0: CRYSTAL STRUCTURE OF THE FIFTH LAMININ G-LIKE MODULE OF THE MOUSE... -

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Basic information

Entry
Database: PDB / ID: 1qu0
TitleCRYSTAL STRUCTURE OF THE FIFTH LAMININ G-LIKE MODULE OF THE MOUSE LAMININ ALPHA2 CHAIN
ComponentsLAMININ ALPHA2 CHAIN
KeywordsMETAL BINDING PROTEIN / BETA SANDWICH / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / regulation of embryonic development / basement membrane ...regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / regulation of embryonic development / basement membrane / positive regulation of cell adhesion / synaptic cleft / regulation of cell migration / axon guidance / animal organ morphogenesis / sarcolemma / neuromuscular junction / collagen-containing extracellular matrix / dendritic spine / cell adhesion / signaling receptor binding / extracellular region
Similarity search - Function
Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / Laminin N-terminal (Domain VI) ...Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin G domain / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Laminin subunit alpha-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsHohenester, E. / Tisi, D. / Talts, J.F. / Timpl, R.
Citation
Journal: Mol.Cell / Year: 1999
Title: The crystal structure of a laminin G-like module reveals the molecular basis of alpha-dystroglycan binding to laminins, perlecan, and agrin.
Authors: Hohenester, E. / Tisi, D. / Talts, J.F. / Timpl, R.
#1: Journal: FEBS Lett. / Year: 1998
Title: Structural analysis and proteolytic processing of recombinant G domain of mouse laminin alpha2 chain
Authors: Talts, J.F. / Mann, K. / Yamada, Y. / Timpl, R.
#2: Journal: J.Anat. / Year: 1998
Title: The role of laminins in basement membrane assembly
Authors: Aumailley, M. / Smyth, N.
History
DepositionJul 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAMININ ALPHA2 CHAIN
B: LAMININ ALPHA2 CHAIN
C: LAMININ ALPHA2 CHAIN
D: LAMININ ALPHA2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,51415
Polymers81,6814
Non-polymers83311
Water4,954275
1
A: LAMININ ALPHA2 CHAIN
B: LAMININ ALPHA2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2097
Polymers40,8402
Non-polymers3685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LAMININ ALPHA2 CHAIN
C: LAMININ ALPHA2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2097
Polymers40,8402
Non-polymers3685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LAMININ ALPHA2 CHAIN
D: LAMININ ALPHA2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3058
Polymers40,8402
Non-polymers4646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LAMININ ALPHA2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6524
Polymers20,4201
Non-polymers2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.220, 112.890, 117.400
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe asymmetric unit contains four copies of the laminin alpha2 LG5 module, which is monomeric in solution

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Components

#1: Protein
LAMININ ALPHA2 CHAIN


Mass: 20420.248 Da / Num. of mol.: 4 / Fragment: LG5 MODULE
Mutation: THE N-TERMINAL APLA SEQUENCE IS DERIVED FROM THE VECTOR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: Q60675
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 3.42 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 2% isopropanol, 100 mM HEPES, 10 mM calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 19 ℃
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMTris-HCl1drop
32.0-2.1 Mammonium sulfate1reservoir
4100 mMNa-HEPES1reservoir
52 %isopropanol1reservoir
610 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. all: 43258 / Num. obs: 43258 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.6
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.11 / % possible all: 85.8
Reflection shell
*PLUS
% possible obs: 85.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.35→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent correction applied
RfactorNum. reflectionSelection details
Rfree0.255 2175 15 thin resolution shells
Rwork0.229 --
all-43258 -
obs-43258 -
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 39 275 5794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 41083
Solvent computation
*PLUS
Displacement parameters
*PLUS

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