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- PDB-1klo: CRYSTAL STRUCTURE OF THREE CONSECUTIVE LAMININ-TYPE EPIDERMAL GRO... -

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Basic information

Entry
Database: PDB / ID: 1klo
TitleCRYSTAL STRUCTURE OF THREE CONSECUTIVE LAMININ-TYPE EPIDERMAL GROWTH FACTOR-LIKE (LE) MODULES OF LAMININ GAMMA1 CHAIN HARBORING THE NIDOGEN BINDING SITE
ComponentsLAMININ
KeywordsGLYCOPROTEIN
Function / homology
Function and homology information


laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / hemidesmosome assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / hair cell differentiation ...laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / hemidesmosome assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / hair cell differentiation / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / hair follicle morphogenesis / positive regulation of muscle cell differentiation / basement membrane / extracellular matrix disassembly / synaptic cleft / positive regulation of cell adhesion / axon guidance / animal organ morphogenesis / neuromuscular junction / neuron projection development / cell migration / chromatin organization / gene expression / protein-containing complex assembly / collagen-containing extracellular matrix / cell adhesion / extracellular region
Similarity search - Function
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 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-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin / Laminin / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Laminin subunit gamma-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsStetefeld, J. / Mayer, U. / Timpl, R. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site.
Authors: Stetefeld, J. / Mayer, U. / Timpl, R. / Huber, R.
#1: Journal: Embo J. / Year: 1994
Title: Two Non-Contiguous Regions Contribute to Nidogen Binding to a Single Egf-Like Motif of the Laminin Gamma 1 Chain
Authors: Poschl, E. / Fox, J.W. / Block, D. / Mayer, U. / Timpl, R.
#2: Journal: Embo J. / Year: 1993
Title: A Single Egf-Like Motif of Laminin is Responsible for High Affinity Nidogen Binding
Authors: Mayer, U. / Nischt, R. / Poschl, E. / Mann, K. / Fukuda, K. / Gerl, M. / Yamada, Y. / Timpl, R.
History
DepositionFeb 2, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAMININ


Theoretical massNumber of molelcules
Total (without water)17,1411
Polymers17,1411
Non-polymers00
Water2,144119
1
A: LAMININ

A: LAMININ

A: LAMININ

A: LAMININ


Theoretical massNumber of molelcules
Total (without water)68,5654
Polymers68,5654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
crystal symmetry operation11_556-x+y,y,-z+11
Unit cell
Length a, b, c (Å)74.570, 74.570, 185.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein LAMININ


Mass: 17141.363 Da / Num. of mol.: 1
Fragment: GAMMA-1 CHAIN, THREE CONSECUTIVE LAMININ-TYPE EPIDERMAL GROWTH FACTOR-LIKE (LE) MODULES
Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P02468
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.59 %
Crystal
*PLUS
Density % sol: 4.1 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17.1 mg/mlprotein1drop
20.62 mMMops1drop
41.0 %(w/v)PEG60001drop
50.07 mM1dropZnSO4
60.75 Mammonium sulfate1reservoir
70.1 Mimidazole1reservoir
3precipitating buffer1drop0.0015 ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 17012 / % possible obs: 91.4 % / Num. measured all: 29004 / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.1972 -
obs0.1972 14983
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 0 119 1298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.36
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.539
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.36
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.539

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