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- PDB-3i70: Long-wavelength structure of NtA -

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Basic information

Entry
Database: PDB / ID: 3i70
TitleLong-wavelength structure of NtA
ComponentsAgrin
Keywordslaminin binding protein / extracelluar matrix / Alternative splicing / Disulfide bond / EGF-like domain / Extracellular matrix / Glycoprotein / Heparan sulfate / Laminin EGF-like domain / Proteoglycan / Secreted
Function / homology
Function and homology information


acetylcholine receptor regulator activity / extracellular matrix of synaptic cleft / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding ...acetylcholine receptor regulator activity / extracellular matrix of synaptic cleft / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding / basal part of cell / transmembrane receptor protein tyrosine kinase activator activity / filopodium assembly / glycosaminoglycan binding / heparan sulfate proteoglycan binding / extracellular matrix binding / positive regulation of filopodium assembly / neuromuscular junction development / receptor clustering / basement membrane / laminin binding / positive regulation of GTPase activity / extracellular matrix / brain development / neuromuscular junction / nervous system development / heparin binding / signaling receptor activity / negative regulation of neuron projection development / actin cytoskeleton organization / cell differentiation / membrane raft / axon / synapse / calcium ion binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Laminin G domain / Laminin-type EGF-like (LE) domain profile. ...NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin EGF domain / : / Laminin-type EGF domain / SEA domain superfamily / Kazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / SEA domain profile. / SEA domain / SEA domain / Laminin G domain profile. / Kazal type serine protease inhibitors / Laminin G domain / Laminin G domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStetefeld, J.
CitationJournal: Protein Sci. / Year: 2009
Title: An interdomain disulfide bridge links the NtA and first FS domain in agrin.
Authors: McFarlane, A.A. / Stetefeld, J.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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: Agrin


Theoretical massNumber of molelcules
Total (without water)14,8341
Polymers14,8341
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.229, 50.710, 54.187
Angle α, β, γ (deg.)90.00, 117.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Agrin


Mass: 14833.925 Da / Num. of mol.: 1 / Fragment: UNP residues 26-153 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Genus: AGRN, AGRIN / References: UniProt: P31696
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.6995 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6995 Å / Relative weight: 1
ReflectionResolution: 2.3→28.06 Å / Num. obs: 8736 / Biso Wilson estimate: 33.5 Å2
Reflection shellHighest resolution: 2.3 Å

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Processing

SoftwareName: CNS / Version: 1.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PXU

1pxu


Resolution: 2.3→27.96 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 871815.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 933 10.7 %RANDOM
Rwork0.221 ---
obs0.221 8736 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.7334 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1-31.61 Å20 Å2-8.79 Å2
2---6.84 Å20 Å2
3----24.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 0 95 1133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.458 162 11.2 %
Rwork0.427 1283 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param

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