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- PDB-1dyk: Laminin alpha 2 chain LG4-5 domain pair -

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Basic information

Entry
Database: PDB / ID: 1dyk
TitleLaminin alpha 2 chain LG4-5 domain pair
ComponentsLAMININ ALPHA 2 CHAIN
KeywordsMETAL BINDING PROTEIN / LAMININ
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 / protein complex involved in cell-matrix adhesion / positive regulation of muscle cell differentiation / regulation of embryonic development / basement membrane / synaptic cleft / positive regulation of cell adhesion ...regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / protein complex involved in cell-matrix adhesion / positive regulation of muscle cell differentiation / regulation of embryonic development / basement membrane / synaptic cleft / positive regulation of cell adhesion / axon guidance / regulation of cell migration / neuromuscular junction / sarcolemma / : / 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 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 G domain / 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 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 1. / EGF-like domain signature 2. / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTisi, D. / Talts, J.F. / Timple, R. / Hohenester, E.
Citation
Journal: Embo J. / Year: 2000
Title: Structure of the C-Terminal Laminin G-Like Domain Pair of the Laminin Alpha 2 Chain Harbouring Binding Sites for Alpha-Dystroglycan and Heparin
Authors: Tisi, D. / Talts, J.F. / Timpl, R. / Hohenester, E.
#1: 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.
#2: Journal: FEBS Lett. / Year: 1998
Title: Structural Analysis and Proteolytic Processing of Recombinant G Domain of Mouse Laminin Alpha 2 Chain
Authors: Talts, J.F. / Mann, K. / Yamada, Y. / Timpl, R.
History
DepositionFeb 1, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAMININ ALPHA 2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8243
Polymers42,7441
Non-polymers802
Water4,522251
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.600, 111.500, 124.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LAMININ ALPHA 2 CHAIN


Mass: 42743.570 Da / Num. of mol.: 1 / Fragment: LAMININ G-LIKE DOMAIN 4-5 PAIR / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: FVB/N / Tissue: EMBRYO / Plasmid: PCEP-PU / Cell (production host): EMRYONIC KIDNEY CELL / Cell line (production host): EBNA-293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q60675
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SWISSPROT SEQUENCE IS TAKEN FROM BERNIER S.M., UTANI A., SUGIYAMA S., DOI T., POLISTINA C., ...THE SWISSPROT SEQUENCE IS TAKEN FROM BERNIER S.M., UTANI A., SUGIYAMA S., DOI T., POLISTINA C., YAMADA Y. MATRIX BIOL. 14:447-455(1995). THE 21 RESIDUES OF THE C-TERMINUS DO NOT MATCH WITH THE SEQUENCE DATABASE REFERENCE PROVIDED. THE COORDINATE SECTION SHOWS COORDINATES TO RESIDUE 3118 WHILE THE SEQUENCE DATABASE ENDS AT RESIDUE 3106 THE CORRECTIONS TO THE SWS ENTRY Q60675 ARE DESCRIBED IN REFERENCE 1 (TALTS ET AL., 1998) OF THIS FILE N-TERMINAL APLA RESIDUES ARE DERIVED FROM THE EXPRESSION SYSTEM VECTOR

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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: 2.87 Å3/Da / Density % sol: 57.19 %
Description: MOLECULAR REPLACEMENT PLUS SIR FROM SM DERIVATIVE
Crystal growpH: 7.5 / Details: pH 7.50
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mM1dropNaCl
4100 mMsodium HEPES1reservoir
52-8 %(v/v)2-propanol1reservoir
619-23 %(w/v)PEG40001reservoir
710 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 CCD / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 31704 / % possible obs: 94.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.139 / % possible all: 93.6
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameClassification
X-PLORrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QU0

1qu0


Resolution: 2→20 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 -10 %RANDOM
Rwork0.233 ---
obs0.233 31676 94.8 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 2 251 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.11
X-RAY DIFFRACTIONx_mcangle_it1.92
X-RAY DIFFRACTIONx_scbond_it3.22
X-RAY DIFFRACTIONx_scangle_it5.24
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2244
Solvent computation
*PLUS
Displacement parameters
*PLUS

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