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- PDB-3pve: Crystal structure of the G2 domain of Agrin from Mus Musculus -

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Basic information

Entry
Database: PDB / ID: 3pve
TitleCrystal structure of the G2 domain of Agrin from Mus Musculus
ComponentsAgrin, Agrin protein
KeywordsTRANSCRIPTION / mRNA splicing / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


negative regulation of P-type sodium:potassium-exchanging transporter activity / : / negative regulation of sodium ion export across plasma membrane / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / positive regulation of protein geranylgeranylation / acetylcholine receptor regulator activity / regulation of axon guidance / Retinoid metabolism and transport ...negative regulation of P-type sodium:potassium-exchanging transporter activity / : / negative regulation of sodium ion export across plasma membrane / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / positive regulation of protein geranylgeranylation / acetylcholine receptor regulator activity / regulation of axon guidance / Retinoid metabolism and transport / ECM proteoglycans / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / regulation of cardiac muscle cell membrane potential / BMP binding / sialic acid binding / plasma membrane organization / tissue development / multicellular organism development / dystroglycan binding / ATPase inhibitor activity / transforming growth factor beta binding / heparan sulfate proteoglycan binding / positive regulation of filopodium assembly / neuromuscular junction development / regulation of GTPase activity / regulation of synapse organization / receptor clustering / positive regulation of protein tyrosine kinase activity / basement membrane / regulation of cardiac muscle contraction / axonal growth cone / regulation of microtubule cytoskeleton organization / synaptic cleft / synapse assembly / positive regulation of GTPase activity / animal organ morphogenesis / regulation of protein phosphorylation / sarcolemma / Golgi lumen / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / positive regulation of protein binding / chemical synaptic transmission / collagen-containing extracellular matrix / transmembrane transporter binding / membrane => GO:0016020 / positive regulation of protein phosphorylation / glutamatergic synapse / synapse / calcium ion binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Domain found in sea urchin sperm protein, enterokinase, agrin / 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 ...Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Domain found in sea urchin sperm protein, enterokinase, agrin / 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 / SEA domain superfamily / Kazal-type serine protease inhibitor domain / Laminin-type EGF 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. / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsSampathkumar, P. / Do, J. / Bain, K. / Freeman, J. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. ...Sampathkumar, P. / Do, J. / Bain, K. / Freeman, J. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the G2 domain of Agrin from Mus Musculus
Authors: Sampathkumar, P.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agrin, Agrin protein
B: Agrin, Agrin protein


Theoretical massNumber of molelcules
Total (without water)40,9892
Polymers40,9892
Non-polymers00
Water4,864270
1
A: Agrin, Agrin protein


Theoretical massNumber of molelcules
Total (without water)20,4941
Polymers20,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Agrin, Agrin protein


Theoretical massNumber of molelcules
Total (without water)20,4941
Polymers20,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.620, 45.580, 51.510
Angle α, β, γ (deg.)72.280, 68.530, 65.440
Int Tables number1
Space group name H-MP1
Detailsmonomer

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Components

#1: Protein Agrin, Agrin protein


Mass: 20494.488 Da / Num. of mol.: 2 / Fragment: G2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Agrin, Agrin (NP_067617) / Plasmid: BS-pSGX4(BS); modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: Q6PCM6, UniProt: A2ASQ1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM sodium acetate, 15% PEG 20000, pH 4.6, Vapor diffusion, sitting drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 19, 2010
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.4→47.16 Å / Num. obs: 57584 / % possible obs: 93.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 13.136 Å2 / Rsym value: 0.093 / Net I/σ(I): 7.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 8386 / Rsym value: 0.491 / % possible all: 92.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
CRANKphasing
RefinementMethod to determine structure: SAD
Starting model: ARP/wARP

Resolution: 1.4→36.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.342 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 2946 5.1 %RANDOM
Rwork0.1921 ---
obs0.194 57556 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 47.33 Å2 / Biso mean: 17.1416 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.01 Å20 Å2
2---0.02 Å20.04 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.4→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 0 270 2843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222730
X-RAY DIFFRACTIONr_bond_other_d0.0010.021827
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9733727
X-RAY DIFFRACTIONr_angle_other_deg0.86834450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.4585370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52122.566113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21715414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4981520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_mcbond_it0.9951.51753
X-RAY DIFFRACTIONr_mcbond_other0.2641.5732
X-RAY DIFFRACTIONr_mcangle_it1.69822776
X-RAY DIFFRACTIONr_scbond_it2.413977
X-RAY DIFFRACTIONr_scangle_it3.9034.5935
LS refinement shellResolution: 1.403→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 234 -
Rwork0.322 3998 -
all-4232 -
obs--100 %

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