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- PDB-1okq: LAMININ ALPHA 2 CHAIN LG4-5 DOMAIN PAIR, CA1 SITE MUTANT -

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Basic information

Entry
Database: PDB / ID: 1okq
TitleLAMININ ALPHA 2 CHAIN LG4-5 DOMAIN PAIR, CA1 SITE MUTANT
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 / basement membrane / regulation of embryonic development / 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 / basement membrane / regulation of embryonic development / 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/attractin EGF domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWizemann, H. / Garbe, J.H.O. / Friedrich, M.V.K. / Timpl, R. / Sasaki, T. / Hohenester, E.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Distinct Requirements for Heparin and Alpha-Dystroglycan Binding Revealed by Structure-Based Mutagenesis of the Laminin Alpha2 Lg4-Lg5 Domain Pair
Authors: Wizemann, H. / Garbe, J.H.O. / Friedrich, M.V.K. / Timpl, R. / Sasaki, T. / Hohenester, E.
#1: Journal: Embo J. / Year: 2000
Title: Structure of the C-Terminal Laminin G-Like Domain Pair of the Laminin Alpha 2 Chain Harbouring Bindin Sites for Alpha-Dystroglycan and Heparin
Authors: Tisi, D. / Talts, J.F. / Timpl, R. / Hohenester, E.
#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
DepositionJul 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 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 13, 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_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_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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAMININ ALPHA 2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6962
Polymers42,6561
Non-polymers401
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.110, 110.734, 123.835
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: 42655.551 Da / Num. of mol.: 1
Fragment: LAMININ G-LIKE DOMAIN 4-5 PAIR, RESIDUES 2729-3093
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: FVB/N / Tissue: EMBRYO / Cell: EMRYONIC KIDNEY CELL / Cell line: EBNA-293 / Plasmid: PCEP-PU / 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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES ASP 2808 ALA, ASP 2876 ALA
Has protein modificationY
Sequence detailsD8080A/D2876A DOUBLE MUTANT THE SWISSPROT SEQUENCE IS TAKEN FROM BERNIER S.M., UTANI A., SUGIYAMA S. ...D8080A/D2876A DOUBLE MUTANT 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 ALPHA 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
20.01 MHEPES1droppH7.5
30.14 M1dropNaCl
410 mM1dropCaCl2
5PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 11824 / % possible obs: 97.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 7.3 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
% possible obs: 97.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DYK

1dyk


Resolution: 2.8→20 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1199 10 %RANDOM
Rwork0.22 ---
obs0.22 11805 97.3 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 1 38 2893
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it3.22
X-RAY DIFFRACTIONc_scangle_it5.24
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. reflection obs: 10606
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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